Rapid Review on Publicly Available Datasets for Health Misinformation Detection

The proliferation of health misinformation in recent years has prompted the development of various methods for detecting and combatting this issue. This review aims to provide an overview of the implementation strategies and characteristics of publicly available datasets that can be used for health misinformation detection. Since 2020, a large number of such datasets have emerged, half of which are focused on COVID-19. Most of the datasets are based on fact-checkable websites, while only a few are annotated by experts. Furthermore, some datasets provide additional information such as social engagement and explanations, which can be utilized to study the spread of misinformation. Overall, these datasets offer a valuable resource for researchers working to combat the spread and consequences of health misinformation.

Transfer Learning for Early Prediction of Adverse Drug Reactions: Docetaxel and Alopecia in Breast Cancer as a Case Study

Transfer Learning (TL) is an approach which has not yet been widely investigated in healthcare, mostly applied in image data. This study outlines a TL pipeline leveraging Individual Case Safety reports (ICSRs) and Electronic Health Records (EHR), applied for the early detection Adverse Drug Reactions (ADR), evaluated using of alopecia and docetaxel on breast cancer patients as use case.

An Integrated Care Platform System (C3-Cloud) for Care Planning, Decision Support, and Empowerment of Patients With Multimorbidity: Protocol for a Technology Trial

Background

There is an increasing need to organize the care around the patient and not the disease, while considering the complex realities of multiple physical and psychosocial conditions, and polypharmacy. Integrated patient-centered care delivery platforms have been developed for both patients and clinicians. These platforms could provide a promising way to achieve a collaborative environment that improves the provision of integrated care for patients via enhanced information and communication technology solutions for semiautomated clinical decision support.

Objective

The Collaborative Care and Cure Cloud project (C3-Cloud) has developed 2 collaborative computer platforms for patients and members of the multidisciplinary team (MDT) and deployed these in 3 different European settings. The objective of this study is to pilot test the platforms and evaluate their impact on patients with 2 or more chronic conditions (diabetes mellitus type 2, heart failure, kidney failure, depression), their informal caregivers, health care professionals, and, to some extent, health care systems.

Methods

This paper describes the protocol for conducting an evaluation of user experience, acceptability, and usefulness of the platforms. For this, 2 “testing and evaluation” phases have been defined, involving multiple qualitative methods (focus groups and surveys) and advanced impact modeling (predictive modeling and cost-benefit analysis). Patients and health care professionals were identified and recruited from 3 partnering regions in Spain, Sweden, and the United Kingdom via electronic health record screening.

Results

The technology trial in this 4-year funded project (2016-2020) concluded in April 2020. The pilot technology trial for evaluation phases 3 and 4 was launched in November 2019 and carried out until April 2020. Data collection for these phases is completed with promising results on platform acceptance and socioeconomic impact. We believe that the phased, iterative approach taken is useful as it involves relevant stakeholders at crucial stages in the platform development and allows for a sound user acceptance assessment of the final product.

Conclusions

Patients with multiple chronic conditions often experience shortcomings in the care they receive. It is hoped that personalized care plan platforms for patients and collaboration platforms for members of MDTs can help tackle the specific challenges of clinical guideline reconciliation for patients with multimorbidity and improve the management of polypharmacy. The initial evaluative phases have indicated promising results of platform usability. Results of phases 3 and 4 were methodologically useful, yet limited due to the COVID-19 pandemic.

Trial Registration

ClinicalTrials.gov NCT03834207; https://clinicaltrials.gov/ct2/show/NCT03834207

International Registered Report Identifier (IRRID)

RR1-10.2196/21994

Encouraging Behavior Changes and Preventing Cardiovascular Diseases Using the Prevent Connect Mobile Health App: Conception and Evaluation of App Quality

Background

Cardiovascular diseases are a major cause of death worldwide. Mobile health apps could help in preventing cardiovascular diseases by improving modifiable risk factors such as eating habits, physical activity levels, and alcohol or tobacco consumption.

Objective

The aim of this study was to design a mobile health app, Prevent Connect, and to assess its quality for (1) assessing patient behavior for 4 cardiovascular risk factors (unhealthy eating, sedentary lifestyle, alcohol, and tobacco consumption) and (2) suggesting personalized recommendations and mobile health interventions for risky behaviors.

Methods

The knowledge base of the app is based on French national recommendations for healthy eating, physical activity, and limiting alcohol and tobacco consumption. It contains a list of patient behaviors and related personalized recommendations and digital health interventions. The interface was designed according to usability principles. Its quality was assessed by a panel of 52 users in a 5-step process: completion of the demographic form, visualization of a short presentation of the app, testing of the app, completion of the user version of the Mobile App Rating Scale (uMARS), and an open group discussion.

Results

This app assesses patient behaviors through specific questionnaires about 4 risk factors (unhealthy eating, sedentary lifestyle, alcohol, and tobacco consumption) and suggests personalized recommendations and digital health interventions for improving behavior. The app was deemed to be of good quality, with a mean uMARS quality score of 4 on a 5-point Likert scale. The functionality and information content of the app were particularly appreciated, with a mean uMARS score above 4. Almost all the study participants appreciated the navigation system and found the app easy to use. More than three-quarters of the study participants found the app content relevant, concise, and comprehensive. The aesthetics and the engagement of the app were also appreciated (uMARS score, 3.7). Overall, 80% (42/52) of the study participants declared that the app helped them to become aware of the importance of addressing health behavior, and 65% (34/52) said that the app helped motivate them to change lifestyle habits.

Conclusions

The app assessed the risky behaviors of the patients and delivered personalized recommendations and digital health interventions for multiple risk factors. The quality of the app was considered to be good, but the impact of the app on behavior changes is yet to be demonstrated and will be assessed in further studies.

Identifying Actionability as a Key Factor for the Adoption of 'Intelligent' Systems for Drug Safety: Lessons Learned from a User-Centred Design Approach

Introduction

Information technology (IT) plays an important role in the healthcare landscape via the increasing digitization of medical data and the use of modern computational paradigms such as machine learning (ML) and knowledge graphs (KGs). These ‘intelligent’ technical paradigms provide a new digital ‘toolkit’ supporting drug safety and healthcare processes, including ‘active pharmacovigilance’. While these technical paradigms are promising, intelligent systems (ISs) are not yet widely adopted by pharmacovigilance (PV) stakeholders, namely the pharma industry, academia/research community, drug safety monitoring organizations, regulatory authorities, and healthcare institutions. The limitations obscuring the integration of ISs into PV activities are multifaceted, involving technical, legal and medical hurdles, and thus require further elucidation.

Objective

We dissect the abovementioned limitations by describing the lessons learned during the design and implementation of the PVClinical platform, a web platform aiming to support the investigation of potential adverse drug reactions (ADRs), emphasizing the use of knowledge engineering (KE) as its main technical paradigm.

Results

To this end, we elaborate on the related ‘business processes’ (i.e. operational processes) and ‘user goals’ identified as part of the PVClinical platform design process based on Design Thinking principles. We also elaborate on key challenges restricting the adoption of such ISs and their integration in the clinical setting and beyond.

Conclusions

We highlight the fact that beyond providing analytics and useful statistics to the end user, ‘actionability’ has emerged as the operational priority identified through the whole process. Furthermore, we focus on the needs for valid, reproducible, explainable and human-interpretable results, stressing the need to emphasize on usability.

Visualising Patterns Associated with Adverse Drug Reactions in French Forums

As social media are an interesting source of information for pharmacovigilance, we implemented a novel visualisation method for pharmacovigilance specialists applied to French discussion forums. A word embedding model was trained on posts to facilitate the identification of patterns associated with adverse drug reactions.

Influence of Connected Health Interventions for Adherence to Cardiovascular Disease Prevention: A Scoping Review

BACKGROUND

Recent health care developments include connected health interventions to improve chronic disease management and/or promote actions reducing aggravating risk factors for conditions such as cardiovascular diseases. Adherence is one of the main challenges for ensuring the correct use of connected health interventions over time.

OBJECTIVE

This scoping review deals with the connected health interventions used in interventional studies, describing the ways in which these interventions and their functions effectively help patients to deal with cardiovascular risk factors over time, in their own environments. The objective is to acquire knowledge and highlight current trends in this field, which is currently both productive and immature.

METHODS

A structured literature review was constructed from Medline-indexed journals in PubMed. We established inclusion criteria relating to three dimensions (cardiovascular risk factors, connected health interventions, and level of adherence). Our initial search yielded 98 articles; 78 were retained after screening on the basis of title and abstract, 49 articles underwent full-text screening, and 24 were finally retained for the analysis, according to preestablished inclusion criteria. We excluded studies of invasive interventions and studies not dealing with digital health. We extracted a description of the connected health interventions from data for the population or end users.

RESULTS

We performed a synthetic analysis of outcomes, based on the distribution of bibliometrics, and identified several connected health interventions and main characteristics affecting adherence. Our analysis focused on three types of user action: to read, to do, and to connect. Finally, we extracted current trends in characteristics: connect, adherence, and influence.

CONCLUSION

Connected health interventions for prevention are unlikely to affect outcomes significantly unless other characteristics and user preferences are considered. Future studies should aim to determine which connected health design combinations are the most effective for supporting long-term changes in behavior and for preventing cardiovascular disease risks.

Supporting Active Pharmacovigilance via IT Tools in the Clinical Setting and Beyond: Regulatory and Management Aspects

Information Technology (IT) could have a prominent role towards the "Active Pharmacovigilance" (AP) paradigm by facilitating the analysis of potential Adverse Drug Reactions (ADRs). PVClinical project aims to build an IT platform enabling the investigation of potential ADRs in the clinical environment and beyond. In this paper, we outline the respective EU regulatory framework and the related Business Processes (BPs), elaborated based on input from clinicians and PV experts as part of the project's "user requirements analysis" phase, highlighting their potential pivotal role in the design of IT tools aiming to support AP.

Decision Support System for Selection of e-Health Interventions

The main goal of this work was to design a decision support system for effective personalized cardiovascular risk prevention: i) to identify behavioral groups associated with clinical risk factors, ii) to provide recommendations associated with the objective to be achieved and iii) to determine the decision-making rules assigning each group to the type of mobile health intervention conveying the most appropriate prevention messages, to help patients to achieve attainable goals. The system is based on an existing data prediction model taking into account specific risky behaviors, clinical risk factors and social status, and it is embedded in a new e-health application. The system is operational. The next step will be the design of a large study to assess improvements in patient adherence to prevention messages through e-health interventions selected by the application.

Classification of the Severity of Adverse Drugs Reactions

This poster presents a non-exhaustive study of machine learning classification algorithms on pharmacovigilance data. In this study, we have taken into account the patient's clinical data such as medical history, medications taken and their indications for prescriptions, and the observed side effects. From these elements we determine whether the patient case is considered serious or not. We show the performances of the different algorithms by their precision, recall and accuracy as well as their learning curves.

Localisation, Personalisation and Delivery of Best Practice Guidelines on an Integrated Care and Cure Cloud Architecture: The C3-Cloud Approach to Managing Multimorbidity

BACKGROUND

C3-Cloud is an integrated care ICT infrastructure offering seamless patient-centered approach to managing multimorbidity, deployed in three European pilot sites. Challenge: The digital delivery of best practice guidelines unified for multimorbidity, customized to local practice, offering the capability to improve patient personalization and benefit.

METHOD

C3-Cloud has adopted a co-production approach to developing unified multimorbidity guidelines, by collating and reconciling best practice guidelines for each condition. Clinical and technical teams at pilot sites and the C3-Cloud consortium worked in tandem to create the specification and technical implementation.

RESULTS

C3-Cloud offers CDSS for diabetes, renal failure, depression and congenital heart failure, with over 300 rules and checks that deliver four best practice guidelines in parallel, customized for each pilot site.

CONCLUSIONS

The process provided a traceable, maintainable and audited digitally delivered collated and reconciled guidelines.

Ontological and Non-Ontological Resources for Associating Medical Dictionary for Regulatory Activities Terms to SNOMED Clinical Terms With Semantic Properties

Background: Formal definitions allow selecting terms (e.g., identifying all terms related to “Infectious disease” using the query “has causative agent organism”) and terminological reasoning (e.g., “hepatitis B” is a “hepatitis” and is an “infectious disease”). However, the standard international terminology Medical Dictionary for Regulatory Activities (MedDRA) used for coding adverse drug reactions in pharmacovigilance databases does not beneficiate from such formal definitions. Our objective was to evaluate the potential of reuse of ontological and non-ontological resources for generating such definitions for MedDRA.

Methods: We developed several methods that collectively allow a semiautomatic semantic enrichment of MedDRA: 1) using MedDRA-to-SNOMED Clinical Terms (SNOMED CT) mappings (available in the Unified Medical Language System metathesaurus or other mapping resources, e.g., the MedDRA preferred term “hepatitis B” is associated to the SNOMED CT concept “type B viral hepatitis”) to extract term definitions (e.g., “hepatitis B” is associated with the following properties: has finding site liver structure, has associated morphology inflammation morphology, and has causative agent hepatitis B virus); 2) using MedDRA labels and lexical/syntactic methods for automatic decomposition of complex MedDRA terms (e.g., the MedDRA systems organ class “blood and lymphatic system disorders” is decomposed in blood system disorders and lymphatic system disorders) or automatic suggestions of properties (e.g., the string “cyclic” in preferred term “cyclic neutropenia” leads to the property has clinical course cyclic).

Results: The Unified Medical Language System metathesaurus was the main ontological resource reusable for generating formal definitions for MedDRA terms. The non-ontological resources (another mapping resource provided by Nadkarni and Darer in 2010 and MedDRA labels) allowed defining few additional preferred terms. While the Ci4SeR tool helped the curator to define 1,935 terms by suggesting potential supplemental relations based on the parents’ and siblings’ semantic definition, defining manually all MedDRA terms remains expensive in time.

Discussion: Several ontological and non-ontological resources are available for associating MedDRA terms to SNOMED CT concepts with semantic properties, but providing manual definitions is still necessary. The ontology of adverse events is a possible alternative but does not cover all MedDRA terms either. Perspectives are to implement more efficient techniques to find more logical relations between SNOMED CT and MedDRA in an automated way.

A Knowledge-Based Platform for Assessing Potential Adverse Drug Reactions at the Point of Care: User Requirements and Design

Even though Adverse Drug Reactions (ADRs) constitute a significant public health issue, there is a lack of Information & Communication Technologies (ICT) tools supporting Pharmacovigilance activities at the point of care. In this paper, we present the rationale of a Web-based platform to address this need. The driving user scenario of the proposed platform refers to a clinician who investigates information for a possible ADR as part of a specific patient treatment. The goal is to facilitate this assessment through appropriate tools for searching various relevant data sources, analysing the acquired data, aggregating the obtained evidence, and offering follow-up ADR monitoring over time in a systematic and user-friendly way. In this regard, we describe the adopted user requirements engineering methodology and illustrate the use of Knowledge Engineering (KE) as the platform's main technical paradigm to enable heterogeneous data integration and handle the complexity of the underlying information processing workflow.

User Driven Design: First Step in Involving Healthcare Consumers and Clinicians in Developing a Collaborative Platform to Prevent Cardiovascular Diseases

To prevent cardiovascular diseases, eHealth solutions may be used as tools, involving health care consumers in the set-up of their prevention plan, a fundamental condition for improving their long-term adherence to the plan. This paper presents the first step in a web platform design aiming to support the co-elaboration by health care consumers and clinicians of personalized prevention plans. Applying a user driven innovation approach, first, a questionnaire and semi-structured interviews were combined to identify clinicians' needs. Then, three focus group sessions with consumers and clinicians were organized to identify their needs, creating the system workflows, its graphical user interface, and its navigation paths, with the best ideas shaped by paper mockups. An interactive mockup was designed including 30 screens (ex. user dashboards, desk for co-elaborating plan). This user driven approach enabled to design not only the technology and its graphical user interface, but also a prevention plan design process.

Mapping the Hyperlink Structure of Diabetes Online Communities

Diabetes is one of the largest global health emergencies of the 21st century. As a chronic disease, diabetes requires continuous medical care and constant patient self-management. Such care involves several stakeholders to improve health outcome and patient quality of life. This paper makes use of World Wide Web network analysis to highlight how stakeholders, providing information about online diabetes communities, link to each other. To achieve this, we capture the network of diabetes related websites as a digital trace of a non-digital phenomenon. Furthermore, this helps us to understand the current situation of diabetes organizations from a digital perspective. The methodology involves state-of-the-art tools to crawl (Hyphe) and visualize (Gephi) topic-sensitive networks. While neither of these tools is new in itself, their combination provides a promising way to analyze chronic disease stakeholders, organizations and communities, representing a large proportion of the knowledge and support diabetes patients have access to nowadays.

User-Centered Design of the C3-Cloud Platform for Elderly with Multiple Diseases - Functional Requirements and Application Testing

The number of patients with multimorbidity has been steadily increasing in the modern aging societies. The European C3-Cloud project provides a multidisciplinary and patient-centered "Collaborative Care and Cure-system" for the management of elderly with multimorbidity, enabling continuous coordination of care activities between multidisciplinary care teams (MDTs), patients and informal caregivers (ICG). In this study various components of the infrastructure were tested to fulfill the functional requirements and the entire system was subjected to an early application testing involving different groups of end-users. MDTs from participating European regions were involved in requirement elicitation and test formulation, resulting in 57 questions, distributed via an internet platform to 48 test participants (22 MDTs, 26 patients) from three pilot sites. The results indicate a high level of satisfaction with all components. Early testing also provided feedback for technical improvement of the entire system, and the paper points out useful evaluation methods.

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.

Semantic Queries Expedite MedDRA Terms Selection Thanks to a Dedicated User Interface: A Pilot Study on Five Medical Conditions

Background: Searching into the MedDRA terminology is usually limited to a hierarchical search, and/or a string search. Our objective was to compare user performances when using a new kind of user interface enabling semantic queries versus classical methods, and evaluating term selection improvement in MedDRA.

Methods: We implemented a forms-based web interface: OntoADR Query Tools (OQT). It relies on OntoADR, a formal resource describing MedDRA terms using SNOMED CT concepts and corresponding semantic relations, enabling terminological reasoning. We then compared time spent on five examples of medical conditions using OQT or the MedDRA web-based browser (MWB), and precision and recall of the term selection.

Results: OntoADR Query Tools allows the user to search in MedDRA: One may enter search criteria by selecting one semantic property from a dropdown list and one or more SNOMED CT concepts related to the range of the chosen property. The user is assisted in building his query: he can add criteria and combine them. Then, the interface displays the set of MedDRA terms matching the query. Meanwhile, on average, the time spent on OQT (about 4 min 30 s) is significantly lower (−35%; p < 0.001) than time spent on MWB (about 7 min). The results of the System Usability Scale (SUS) gave a score of 62.19 for OQT (rated as good). We also demonstrated increased precision (+27%; p = 0.01) and recall (+34%; p = 0.02). Computed “performance” (correct terms found per minute) is more than three times better with OQT than with MWB.

Discussion: This pilot study establishes the feasibility of our approach based on our initial assumption: performing MedDRA queries on the five selected medical conditions, using terminological reasoning, expedites term selection, and improves search capabilities for pharmacovigilance end users. Evaluation with a larger number of users and medical conditions are required in order to establish if OQT is appropriate for the needs of different user profiles, and to check if conclusions can be extended to other kinds of medical conditions. The application is currently limited by the non-exhaustive coverage of MedDRA by OntoADR, but nevertheless shows good performance which encourages continuing in the same direction.

Quantitative analysis of manual annotation of clinical text samples

BACKGROUND

Semantic interoperability of eHealth services within and across countries has been the main topic in several research projects. It is a key consideration for the European Commission to overcome the complexity of making different health information systems work together. This paper describes a study within the EU-funded project ASSESS CT, which focuses on assessing the potential of SNOMED CT as core reference terminology for semantic interoperability at European level.

OBJECTIVE

This paper presents a quantitative analysis of the results obtained in ASSESS CT to determine the fitness of SNOMED CT for semantic interoperability.

METHODS

The quantitative analysis consists of concept coverage, term coverage and inter-annotator agreement analysis of the annotation experiments related to six European languages (English, Swedish, French, Dutch, German and Finnish) and three scenarios: (i) ADOPT, where only SNOMED CT was used by the annotators; (ii) ALTERNATIVE, where a fixed set of terminologies from UMLS, excluding SNOMED CT, was used; and (iii) ABSTAIN, where any terminologies available in the current national infrastructure of the annotators' country were used. For each language and each scenario, we configured the different terminology settings of the annotation experiments.

RESULTS

There was a positive correlation between the number of concepts in each terminology setting and their concept and term coverage values. Inter-annotator agreement is low, irrespective of the terminology setting.

CONCLUSIONS

No significant differences were found between the analyses for the three scenarios, but availability of SNOMED CT for the assessed language is associated with increased concept coverage. Terminology setting size and concept and term coverage correlate positively up to a limit where more concepts do not significantly impact the coverage values. The results did not confirm the hypothesis of an inverse correlation between concept coverage and IAA due to a lower amount of choices available. The overall low IAA results pose a challenge for interoperability and indicate the need for further research to assess whether consistent terminology implementation is possible across Europe, e.g., improving term coverage by adding localized versions of the selected terminologies, analysing causes of low inter-annotator agreement, and improving tooling and guidance for annotators. The much lower term coverage for the Swedish version of SNOMED CT compared to English together with the similarly high concept coverage obtained with English and Swedish SNOMED CT reflects its relevance as a hub to connect user interface terminologies and serving a variety of user needs.

Federating patients identities: the case of rare diseases

BACKGROUND

Patient information in rare disease registries is generally collected from numerous data sources, necessitating the data to be federated. In addition, data for research purposes must be de-identified. Transforming nominative data into de-identified data is thus a key issue, while minimizing the number of identity duplicates. We propose a method enabling patient identity federation and rare disease data de-identification while preserving the pertinence of the provided data.

RESULTS

We developed a rare disease patient identifier. The IdMR generation process is a three-phased algorithm involving a hash function to irreversibly de-identify nominative patient data, including those of foetuses. This process minimizes collision risks and reduces variability for the purpose of identity federation. The IdMR was generated for 360,000 patients of the CEMARA database. It allowed identity federation of 1771 duplicated files. No collisions were introduced.

CONCLUSION

We examined and discussed the risks of collisions and the creation of duplicates as well as the risks of patient re-identification. We discussed our choice of nominative input information in light of that used by other patient identification solutions. The IdMR is a patient identifier that enables identity federation and file linkage. The simplicity of the algorithm and the universality and stability of the input data make it a good candidate for European cross-border rare disease projects.

Semantic interoperability challenges to process large amount of data perspectives in forensic and legal medicine

This article is a position paper dealing with semantic interoperability challenges. It addresses the Variety and Veracity dimensions when integrating, sharing and reusing large amount of heterogeneous data for data analysis and decision making applications in the healthcare domain. Many issues are raised by the necessity to conform Big Data to interoperability standards. We discuss how semantics can contribute to the improvement of information sharing and address the problem of data mediation with domain ontologies. We then introduce the main steps for building domain ontologies as they could be implemented in the context of Forensic and Legal medicine. We conclude with a particular emphasis on the current limitations in standardisation and the importance of knowledge formalization.

OpenPVSignal: Advancing Information Search, Sharing and Reuse on Pharmacovigilance Signals via FAIR Principles and Semantic Web Technologies

Signal detection and management is a key activity in pharmacovigilance (PV). When a new PV signal is identified, the respective information is publicly communicated in the form of periodic newsletters or reports by organizations that monitor and investigate PV-related information (such as the World Health Organization and national PV centers). However, this type of communication does not allow for systematic access, discovery and explicit data interlinking and, therefore, does not facilitate automated data sharing and reuse. In this paper, we present OpenPVSignal, a novel ontology aiming to support the semantic enrichment and rigorous communication of PV signal information in a systematic way, focusing on two key aspects: (a) publishing signal information according to the FAIR (Findable, Accessible, Interoperable, and Re-usable) data principles, and (b) exploiting automatic reasoning capabilities upon the interlinked PV signal report data. OpenPVSignal is developed as a reusable, extendable and machine-understandable model based on Semantic Web standards/recommendations. In particular, it can be used to model PV signal report data focusing on: (a) heterogeneous data interlinking, (b) semantic and syntactic interoperability, (c) provenance tracking and (d) knowledge expressiveness. OpenPVSignal is built upon widely-accepted semantic models, namely, the provenance ontology (PROV-O), the Micropublications semantic model, the Web Annotation Data Model (WADM), the Ontology of Adverse Events (OAE) and the Time ontology. To this end, we describe the design of OpenPVSignal and demonstrate its applicability as well as the reasoning capabilities enabled by its use. We also provide an evaluation of the model against the FAIR data principles. The applicability of OpenPVSignal is demonstrated by using PV signal information published in: (a) the World Health Organization's Pharmaceuticals Newsletter, (b) the Netherlands Pharmacovigilance Centre Lareb Web site and (c) the U.S. Food and Drug Administration (FDA) Drug Safety Communications, also available on the FDA Web site.

Descriptions of Adverse Drug Reactions Are Less Informative in Forums Than in the French Pharmacovigilance Database but Provide More Unexpected Reactions

Background: Social media have drawn attention for their potential use in Pharmacovigilance. Recent work showed that it is possible to extract information concerning adverse drug reactions (ADRs) from posts in social media. The main objective of the Vigi4MED project was to evaluate the relevance and quality of the information shared by patients on web forums about drug safety and its potential utility for pharmacovigilance.

Methods: After selecting websites of interest, we manually evaluated the relevance of the content of posts for pharmacovigilance related to six drugs (agomelatine, baclofen, duloxetine, exenatide, strontium ranelate, and tetrazepam). We compared forums to the French Pharmacovigilance Database (FPVD) to (1) evaluate whether they contained relevant information to characterize a pharmacovigilance case report (patient’s age and sex; treatment indication, dose and duration; time-to-onset (TTO) and outcome of the ADR, and drug dechallenge and rechallenge) and (2) perform impact analysis (nature, seriousness, unexpectedness, and outcome of the ADR).

Results: The cases in the FPVD were significantly more informative than posts in forums for patient description (age, sex), treatment description (dose, duration, TTO), and outcome of the ADR, but the indication for the treatment was more often found in forums. Cases were more often serious in the FPVD than in forums (46% vs. 4%), but forums more often contained an unexpected ADR than the FPVD (24% vs. 17%). Moreover, 197 unexpected ADRs identified in forums were absent from the FPVD and the distribution of the MedDRA System Organ Classes (SOCs) was different between the two data sources.

Discussion: This study is the first to evaluate if patients’ posts may qualify as potential and informative case reports that should be stored in a pharmacovigilance database in the same way as case reports submitted by health professionals. The posts were less informative (except for the indication) and focused on less serious ADRs than the FPVD cases, but more unexpected ADRs were presented in forums than in the FPVD and their SOCs were different. Thus, web forums should be considered as a secondary, but complementary source for pharmacovigilance.

Evaluation Criteria of Noninvasive Telemonitoring for Patients With Heart Failure: Systematic Review

BACKGROUND

Telemonitoring can improve heart failure (HF) management, but there is no standardized evaluation framework to comprehensively evaluate its impact.

OBJECTIVE

Our objectives were to list the criteria used in published evaluations of noninvasive HF telemonitoring projects, describe how they are used in the evaluation studies, and organize them into a consistent scheme.

METHODS

Articles published from January 1990 to August 2015 were obtained through MEDLINE, Web of Science, and EMBASE. Articles were eligible if they were original reports of a noninvasive HF telemonitoring evaluation study in the English language. Studies of implantable telemonitoring devices were excluded. Each selected article was screened to extract the description of the telemonitoring project and the evaluation process and criteria. A qualitative synthesis was performed.

RESULTS

We identified and reviewed 128 articles leading to 52 evaluation criteria classified into 6 dimensions: clinical, economic, user perspective, educational, organizational, and technical. The clinical and economic impacts were evaluated in more than 70% of studies, whereas the educational, organizational, and technical impacts were studied in fewer than 15%. User perspective was the most frequently covered dimension in the development phase of telemonitoring projects, whereas clinical and economic impacts were the focus of later phases.

CONCLUSIONS

Telemonitoring evaluation frameworks should cover all 6 dimensions appropriately distributed along the telemonitoring project lifecycle. Our next goal is to build such a comprehensive evaluation framework for telemonitoring and test it on an ongoing noninvasive HF telemonitoring project.

Building a Knowledge-Based Tool for Auto-Assessing the Cardiovascular Risk

The prevention of cardiovascular diseases needs first to quantify the cardiovascular risk. To estimate this risk, French national health authorities provided clinical practice guidelines extending the existing European SCORE, which doesn't include all the cardiovascular risk factors (e.g. diabetes). Hence, French national clinical practice guidelines to quantify the cardiovascular risk is able to deal with more clinical situations than the SCORE. The goal of this paper is to formalize knowledge extracted from these guidelines and implement the rules so that they can be used into an auto-assessing tool of cardiovascular risk. Formalization followed five steps and was conducted under the guidance of medical experts. It resulted into a decision tree fed by eight decision variables. Evaluation of the accuracy of the decision tree showed 80% of agreement with an expert in medical informatics in predicting the cardiovascular risk level for 15 different clinical situations. Discrepancies correspond to the knowledge gaps within Clinical Practice Guidelines. We intend to extend the implementation of the decision tree to a complete tool, for allowing patient to auto-assess their cardiovascular risk. This tool will be integrated into a platform providing recommendations adapted to the calculated level of cardiovascular risk.

Modular Knowledge-Based Decision Support System Dedicated to a Cooperative Decision to Prevent Cardiovascular Diseases

Despite the success of artificial intelligence solutions in the recent years, physicians are still reticent to use integrated functionalities to support their decision. Methods used to create these functionalities can be divided into two groups, each being associated to different questions. Data-based methods are seen as black boxes for which it is impossible to understand how the decision is taken; knowledge-based methods need to rely on formalized knowledge sources on the basis of evidence, which can be discussed and criticized by physicians for their use in real life. This paper presents a new modular decision support system for the prevention of cardiovascular diseases, based on knowledge and on cooperative decision between the patient and the physician. The decision support system is based on two layers: (i) the first layer is a knowledge-based module which generates automatically patient profile, and prevention strategies associated to the profile; (ii) the second layer is a dynamic collaborative graphic user interface which displayed information about the risks of treatment adherence failure, personalized motivation and follow-up strategies. In the future, we aim at assessing the platform in real life.

Parallel Design of Browsing Scheme and Data Model for Multi-Level Hierarchical Application Devoted to Management of Patient with Infectious Disease in Primary Care

Many decision systems are based on a hierarchical approach, enriching the known context used to finally choose the right potential action. Designing the scheme for browsing the clinical guidelines is a task devoted to expert in infectious diseases. Designing the data model is a task devoted to the expert in data modeling. As a consequence, browsing scheme and data model generally differ in terms of abstraction levels. While the browsing scheme proposes to navigate into depth, the data model stays flat. We propose here a novel method to design in parallel the browsing scheme and the data model so that both of them reflect the different abstraction levels in decision process.

From Patient Discharge Summaries to an Ontology for Psychiatry

Psychiatry aims at detecting symptoms, providing diagnoses and treating mental disorders. We developed ONTOPSYCHIA, an ontology for psychiatry in three modules: social and environmental factors of mental disorders, mental disorders, and treatments. The use of ONTOPSYCHIA, associated with dedicated tools, will facilitate semantic research in Patient Discharge Summaries (PDS). To develop the first module of the ontology we propose a PDS text analysis in order to explicit psychiatry concepts. We decided to set aside classifications during the construction of the modu le, to focus only on the information contained in PDS (bottom-up approach) and to return to domain classifications solely for the enrichment phase (top-down approach). Then, we focused our work on the development of the LOVMI methodology (Les Ontologies Validées par Méthode Interactive - Ontologies Validated by Interactive Method), which aims to provide a methodological framework to validate the structure and the semantic of an ontology.

Design of a Visual Interface for Comparing Antibiotics Using Rainbow Boxes

Non-optimal prescriptions of antibiotics have a negative impact on patients and population. Clinical practice guidelines are not always followed by doctors because the rationale of the recommendations is not always clear and can be difficult to understand. In this paper, we propose a new approach consisting in presenting the properties of antibiotics for allowing doctors to compare them and choose the most appropriate one. For that, we used and extended rainbow boxes, a new technique for overlapping set visualization. We tested our approach on 11 clinical situations related to urinary infections, and assessed the simplicity, the interest and utility with 11 doctors. 10 of them found that this approach was interesting and useful in clinical practice. Further studies are needed to confirm this preliminary work.

Exploiting heterogeneous publicly available data sources for drug safety surveillance: computational framework and case studies

OBJECTIVE

Driven by the need of pharmacovigilance centres and companies to routinely collect and review all available data about adverse drug reactions (ADRs) and adverse events of interest, we introduce and validate a computational framework exploiting dominant as well as emerging publicly available data sources for drug safety surveillance.

METHODS

Our approach relies on appropriate query formulation for data acquisition and subsequent filtering, transformation and joint visualization of the obtained data. We acquired data from the FDA Adverse Event Reporting System (FAERS), PubMed and Twitter. In order to assess the validity and the robustness of the approach, we elaborated on two important case studies, namely, clozapine-induced cardiomyopathy/myocarditis versus haloperidol-induced cardiomyopathy/myocarditis, and apixaban-induced cerebral hemorrhage.

RESULTS

The analysis of the obtained data provided interesting insights (identification of potential patient and health-care professional experiences regarding ADRs in Twitter, information/arguments against an ADR existence across all sources), while illustrating the benefits (complementing data from multiple sources to strengthen/confirm evidence) and the underlying challenges (selecting search terms, data presentation) of exploiting heterogeneous information sources, thereby advocating the need for the proposed framework.

CONCLUSIONS

This work contributes in establishing a continuous learning system for drug safety surveillance by exploiting heterogeneous publicly available data sources via appropriate support tools.

[Automated grouping of terms associated to cardiac valve fibrosis in MedDRA]

AIM

To propose an alternative approach for building custom groupings of terms that complements the usual approach based on both hierarchical method (selection of reference groupings in medical dictionary for regulatory activities [MedDRA]) and/or textual method (string search), for case reports extraction from a pharmacovigilance database in response to a safety problem. Here we take cardiac valve fibrosis as an example.

METHODS

The list of terms obtained by an automated approach, based on querying ontology of adverse drug reactions (OntoADR), a knowledge base defining MedDRA terms through relationships with systematized nomenclature of medicine-clinical terms (SNOMED CT) concepts, was compared with the reference list consisting of 53 preferred terms obtained by hierarchical and textual method. Two queries were performed on OntoADR by using a dedicated software: OntoADR query tools. Both queries excluded congenital diseases, and included a procedure or an auscultation method performed on cardiac valve structures. Query 1 also considered MedDRA terms related to fibrosis, narrowing or calcification of heart valves, and query 2 MedDRA terms described according to one of these four SNOMED CT terms: "Insufficiency", "Valvular sclerosis", "Heart valve calcification" or "Heart valve stenosis".

RESULTS

The reference grouping consisted of 53 MedDRA preferred terms. Our automated method achieved recall of 79% and precision of 100% for query 1 privileging morphological abnormalities, and recall of 100% and precision of 96% for query 2 privileging functional abnormalities.

CONCLUSION

An alternative approach to MedDRA reference groupings for building custom groupings is feasible for cardiac valve fibrosis. OntoADR is still in development. Its application to other adverse reactions would require significant work for a knowledge engineer to define every MedDRA term, but such definitions could then be queried as many times as necessary by pharmacovigilance professionals.

Cross border semantic interoperability for clinical research: the EHR4CR semantic resources and services

With the development of platforms enabling the use of routinely collected clinical data in the context of international clinical research, scalable solutions for cross border semantic interoperability need to be developed. Within the context of the IMI EHR4CR project, we first defined the requirements and evaluation criteria of the EHR4CR semantic interoperability platform and then developed the semantic resources and supportive services and tooling to assist hospital sites in standardizing their data for allowing the execution of the project use cases. The experience gained from the evaluation of the EHR4CR platform accessing to semantically equivalent data elements across 11 European participating EHR systems from 5 countries demonstrated how far the mediation model and mapping efforts met the expected requirements of the project. Developers of semantic interoperability platforms are beginning to address a core set of requirements in order to reach the goal of developing cross border semantic integration of data.

OntoADR a semantic resource describing adverse drug reactions to support searching, coding, and information retrieval

INTRODUCTION

Efficient searching and coding in databases that use terminological resources requires that they support efficient data retrieval. The Medical Dictionary for Regulatory Activities (MedDRA) is a reference terminology for several countries and organizations to code adverse drug reactions (ADRs) for pharmacovigilance. Ontologies that are available in the medical domain provide several advantages such as reasoning to improve data retrieval. The field of pharmacovigilance does not yet benefit from a fully operational ontology to formally represent the MedDRA terms. Our objective was to build a semantic resource based on formal description logic to improve MedDRA term retrieval and aid the generation of on-demand custom groupings by appropriately and efficiently selecting terms: OntoADR.

METHODS

The method consists of the following steps: (1) mapping between MedDRA terms and SNOMED-CT, (2) generation of semantic definitions using semi-automatic methods, (3) storage of the resource and (4) manual curation by pharmacovigilance experts.

RESULTS

We built a semantic resource for ADRs enabling a new type of semantics-based term search. OntoADR adds new search capabilities relative to previous approaches, overcoming the usual limitations of computation using lightweight description logic, such as the intractability of unions or negation queries, bringing it closer to user needs. Our automated approach for defining MedDRA terms enabled the association of at least one defining relationship with 67% of preferred terms. The curation work performed on our sample showed an error level of 14% for this automated approach. We tested OntoADR in practice, which allowed us to build custom groupings for several medical topics of interest.

DISCUSSION

The methods we describe in this article could be adapted and extended to other terminologies which do not benefit from a formal semantic representation, thus enabling better data retrieval performance. Our custom groupings of MedDRA terms were used while performing signal detection, which suggests that the graphical user interface we are currently implementing to process OntoADR could be usefully integrated into specialized pharmacovigilance software that rely on MedDRA.

Towards data integration automation for the French rare disease registry

Building a medical registry upon an existing infrastructure and rooted practices is not an easy task. It is the case for the BNDMR project, the French rare disease registry, that aims to collect administrative and medical data of rare disease patients seen in different hospitals. To avoid duplicating data entry for health professionals, the project plans to deploy connectors with the existing systems to automatically retrieve data. Given the data heterogeneity and the large number of source systems, the automation of connectors creation is required. In this context, we propose a methodology that optimizes the use of existing alignment approaches in the data integration processes. The generated mappings are formalized in exploitable mapping expressions. Following this methodology, a process has been experimented on specific data types of a source system: Boolean and predefined lists. As a result, effectiveness of the used alignment approach has been enhanced and more good mappings have been detected. Nonetheless, further improvements could be done to deal with the semantic issue and process other data types.

Adverse Drug Reaction Identification and Extraction in Social Media: A Scoping Review

Background

The underreporting of adverse drug reactions (ADRs) through traditional reporting channels is a limitation in the efficiency of the current pharmacovigilance system. Patients’ experiences with drugs that they report on social media represent a new source of data that may have some value in postmarketing safety surveillance.

Objective

A scoping review was undertaken to explore the breadth of evidence about the use of social media as a new source of knowledge for pharmacovigilance.

Methods

Daubt et al’s recommendations for scoping reviews were followed. The research questions were as follows: How can social media be used as a data source for postmarketing drug surveillance? What are the available methods for extracting data? What are the different ways to use these data? We queried PubMed, Embase, and Google Scholar to extract relevant articles that were published before June 2014 and with no lower date limit. Two pairs of reviewers independently screened the selected studies and proposed two themes of review: manual ADR identification (theme 1) and automated ADR extraction from social media (theme 2). Descriptive characteristics were collected from the publications to create a database for themes 1 and 2.

Results

Of the 1032 citations from PubMed and Embase, 11 were relevant to the research question. An additional 13 citations were added after further research on the Internet and in reference lists. Themes 1 and 2 explored 11 and 13 articles, respectively. Ways of approaching the use of social media as a pharmacovigilance data source were identified.

Conclusions

This scoping review noted multiple methods for identifying target data, extracting them, and evaluating the quality of medical information from social media. It also showed some remaining gaps in the field. Studies related to the identification theme usually failed to accurately assess the completeness, quality, and reliability of the data that were analyzed from social media. Regarding extraction, no study proposed a generic approach to easily adding a new site or data source. Additional studies are required to precisely determine the role of social media in the pharmacovigilance system.

Computational approaches for pharmacovigilance signal detection: toward integrated and semantically-enriched frameworks

Computational signal detection constitutes a key element of postmarketing drug monitoring and surveillance. Diverse data sources are considered within the 'search space' of pharmacovigilance scientists, and respective data analysis methods are employed, all with their qualities and shortcomings, towards more timely and accurate signal detection. Recent systematic comparative studies highlighted not only event-based and data-source-based differential performance across methods but also their complementarity. These findings reinforce the arguments for exploiting all possible information sources for drug safety and the parallel use of multiple signal detection methods. Combinatorial signal detection has been pursued in few studies up to now, employing a rather limited number of methods and data sources but illustrating well-promising outcomes. However, the large-scale realization of this approach requires systematic frameworks to address the challenges of the concurrent analysis setting. In this paper, we argue that semantic technologies provide the means to address some of these challenges, and we particularly highlight their contribution in (a) annotating data sources and analysis methods with quality attributes to facilitate their selection given the analysis scope; (b) consistently defining study parameters such as health outcomes and drugs of interest, and providing guidance for study setup; (c) expressing analysis outcomes in a common format enabling data sharing and systematic comparisons; and (d) assessing/supporting the novelty of the aggregated outcomes through access to reference knowledge sources related to drug safety. A semantically-enriched framework can facilitate seamless access and use of different data sources and computational methods in an integrated fashion, bringing a new perspective for large-scale, knowledge-intensive signal detection.

A "pivot" Model to set up Large Scale Rare Diseases Information Systems: Application to the Fibromuscular Dysplasia Registry

The SIR-FMD project is a partnership between the Department of Genetics and Reference Centre for Rare Vascular Diseases at the Georges Pompidou European Hospital in Paris and the Medical Informatics and Knowledge Engineering Laboratory of Inserm. Its aim is to use an ontological approach to implement an information system for the French Fibromuscular Dysplasia Registry. The existing data was dispersed in numerous databases, which had been created independently. These databases have different structures and contain data of diverse quality. The project aims to provide generic solutions for the management of the communication of medical data. The secondary objective is to demonstrate the applicability of these generic solutions in the field of rare diseases (RD) in an operational context. The construction of the French FMD registry was a multistep process. A secure platform has been available since the beginning of November 2013. The medical records of 471 patients from the initial dataset provided by the HEGP-Paris, France have been included, and are accessible from a secure user account. Users are organized into a collaborative group, and can access patient groups. Each electronic patient record contains more than 2,200 items. The problem of semantic interoperability has become one of the major challenges for the development of applications requiring the sharing and reuse of data. The information system component of the SIR-FMD project has a direct impact on the standardisation of coding of rare diseases and thereby contributes to the development of e-Health.

Building a Semantic Interoperability Framework for Care and Research in Fibromuscular Dysplasia

Identifying patients with Fibromuscular Dysplasia (FMD) at the international level will have considerable value for understanding the epidemiology, clinical manifestations and susceptible genes in this arterial disease, but also for identifying eligible patients in clinical trials or cohorts. We present a two-step methodology to create a general semantic interoperability framework allowing access and comparison of distributed data over various nations, languages, formats and databases.

METHODS

The first step is to develop a pivot multidimensional model based on a core dataset to harmonize existing heterogeneous data sources. The second step is to align the model to additional data, semantically related to FMD and collected currently in various registries. We present the results of the first step that has been fully completed with the validation and implementation of the model in a dedicated information system (SIR-FMD). We discuss the current achievements for step 2 and the extensibility of the methodology in the context of other rare diseases.

Personalized decision support system based on clinical practice guidelines

Personalized medicine is a broad and rapidly advancing field of health care that is informed by each person's unique clinical, genetic, genomic, and environmental information. Health care that embraces personalized medicine is an integrated, coordinated, evidence based approach to individualizing patient care across the continuum. It is very important to make the right treatment decision but before that to obtain a good diagnosis. There are several clinical forms of disease whose symptoms vary depending on the age and etiology. In this study, we investigated and evaluated a model framework, for personalized diagnostic decisions, based on Case Based Fuzzy Cognitive Map (CBFCM, a cognitive process applying the main features of fuzzy logic and neural processors to situations involving imprecision and uncertain descriptions, in a similar way to intuitive human reasoning. We explored the use of this method for modelling clinical practice guidelines.

Ethical, Legal and Social Issues related to the health data-warehouses: re-using health data in the research and public health research

Research derived from the application of information and communication technologies in medicine operates in a context involving the globalization of collecting, sharing, storage, transfer and re-use of personal health data. Health data computerization within Clinical Information Systems (as Electronic Healthcare Records) should allow the re-use of health data for clinical research and public health purposes. One of the objects allowing the integration of healthcare and research information systems is the health data-warehouse (DWH). However, ethical-legal frameworks in force are not adapted to these DWHs because they were not conceived for re-using data in a different context than the one of their acquisition. For that matter, access modalities to data-warehouses must ensure the respect of patients' rights: information to the patient, as well as confidentiality and security. Through a bibliography research, some Ethical, legal and Social Issues (ELSI) have been identified: Patients' rights Modalities of implementation of the DWs; Solidarity and common good; Transparency and Trust. Comparative analysis between the Directive 95/46/CE and the "Proposal for regulation on protection of individuals with regard to the processing of personal data" shows that this regulation pretends allowing the re-use of key-coded data when aimed at a scientific purpose. However, since this new regulation does not align with the ethical and legal requirements at an operational level, a Code of practice on secondary use of Medical Data in scientific Research Projects has been developed at the European Level. This Code provides guidance for Innovative Medicine Initiative (IMI) and will help to propose practical solutions to overcome the issue of the re-use of data for research purposes.

Formalizing MedDRA to support semantic reasoning on adverse drug reaction terms

Although MedDRA has obvious advantages over previous terminologies for coding adverse drug reactions and discovering potential signals using data mining techniques, its terminological organization constrains users to search terms according to predefined categories. Adding formal definitions to MedDRA would allow retrieval of terms according to a case definition that may correspond to novel categories that are not currently available in the terminology. To achieve semantic reasoning with MedDRA, we have associated formal definitions to MedDRA terms in an OWL file named OntoADR that is the result of our first step for providing an "ontologized" version of MedDRA. MedDRA five-levels original hierarchy was converted into a subsumption tree and formal definitions of MedDRA terms were designed using several methods: mappings to SNOMED-CT, semi-automatic definition algorithms or a fully manual way. This article presents the main steps of OntoADR conception process, its structure and content, and discusses problems and limits raised by this attempt to "ontologize" MedDRA.

Automatic annotation of ICD-to-MedDRA mappings with SKOS predicates

Robust alignments between ICD and MedDRA are essential to enable the secondary use of clinical data for pharmacovigilance research. UMLS makes available ICD-to-MedDRA mappings, but they are only poorly specified, which introduces difficulties when exploited in an automatic way. SKOS vocabulary can help achieve quality and machine-processable mappings. We have developed an algorithm based on several simple rules which annotates automatically ICD-to-MedDRA mappings with SKOS predicates. The method was tested and evaluated on a sample of ICD-10-to MedDRA mappings extracted from UMLS. The algorithm demonstrated satisfying performances, especially for skos:exactMatch properties, which suggests that automatic methods can be used to improve the quality of terminology mappings.

Towards an automatic harmonization of the representation of medical reports to assess their similarities

Numerous hospitals contain unexploited knowledge deposits. These often take the form of unstructured records with heterogeneous content, which, at various levels of those organizations, register past cases. Those records are for instance patient medical records. Accessing the knowledge and experience they gather would help us to handle present cases. We present here a method to normalize textual reports in foetopathology in order to constitute a proper case base that will be the target of case-based reasoning techniques. Statistics of noise and silence generated by this method on 10 cases are presented.

Ci4SeR--curation interface for semantic resources--evaluation with adverse drug reactions

Evaluation and validation have become a crucial problem for the development of semantic resources. We developed Ci4SeR, a Graphical User Interface to optimize the curation work (not taking into account structural aspects), suitable for any type of resource with lightweight description logic. We tested it on OntoADR, an ontology of adverse drug reactions. A single curator has reviewed 326 terms (1020 axioms) in an estimated time of 120 hours (2.71 concepts and 8.5 axioms reviewed per hour) and added 1874 new axioms (15.6 axioms per hour). Compared with previous manual endeavours, the interface allows increasing the speed-rate of reviewed concepts by 68% and axiom addition by 486%. A wider use of Ci4SeR would help semantic resources curation and improve completeness of knowledge modelling.

Formalizing mappings to optimize automated schema alignment: application to rare diseases

In the era of data sharing and systems interoperability, the automation of data schema alignment has become a priority. Discovering data mappings is the aim of many alignment approaches that have been described in the literature and the effectiveness of which depends on data specifications. In this context, we propose a method for mappings formalization that allows automated data integration processes optimization. This method, involving both data element level and value element level, allows an automated inference of mappings expressed by rules. In this paper, we start by describing the methods used to achieve this mappings formalization. Then, we explain how it has been validated by characterizing data from two use cases. We end up by discussing the objectives of the proposed formalization.

Application of probabilistic and fuzzy cognitive approaches in semantic web framework for medical decision support

This study aimed to focus on medical knowledge representation and reasoning using the probabilistic and fuzzy influence processes, implemented in the semantic web, for decision support tasks. Bayesian belief networks (BBNs) and fuzzy cognitive maps (FCMs), as dynamic influence graphs, were applied to handle the task of medical knowledge formalization for decision support. In order to perform reasoning on these knowledge models, a general purpose reasoning engine, EYE, with the necessary plug-ins was developed in the semantic web. The two formal approaches constitute the proposed decision support system (DSS) aiming to recognize the appropriate guidelines of a medical problem, and to propose easily understandable course of actions to guide the practitioners. The urinary tract infection (UTI) problem was selected as the proof-of-concept example to examine the proposed formalization techniques implemented in the semantic web. The medical guidelines for UTI treatment were formalized into BBN and FCM knowledge models. To assess the formal models' performance, 55 patient cases were extracted from a database and analyzed. The results showed that the suggested approaches formalized medical knowledge efficiently in the semantic web, and gave a front-end decision on antibiotics' suggestion for UTI.