Ontology-Based CMS News Authoring Environment

This paper describes the specification, modelling and design of an ontology-based news authoring environment for the Semantic Web, that takes into account the construction and use of an ontology of the Zika disease. CMSs are being adapted in order to receive semantic features, such as automatic generations of keywords, semantic annotation and tagging, content reviewing etc. We present here the infrastructure designed to foster research on semantic CMSs as well as semantic web technologies that can be integrated into an ontology-based news authoring environment

Knowledge Organization Systems for Systematic Chemical Assessments

BACKGROUND: Although the implementation of systematic review and evidence mapping methods stands to improve the transparency and accuracy of chemical assessments, they also accentuate the challenges that assessors face in ensuring they have located and included all the evidence that is relevant to evaluating the potential health effects an exposure might be causing. This challenge of information retrieval can be characterized in terms of "semantic" and "conceptual" factors that render chemical assessments vulnerable to the streetlight effect. OBJECTIVES: This commentary presents how controlled vocabularies, thesauruses, and ontologies contribute to overcoming the streetlight effect in information retrieval, making up the key components of Knowledge Organization Systems (KOSs) that enable more systematic access to assessment-relevant information than is currently achievable. The concept of Adverse Outcome Pathways is used to illustrate what a general KOS for use in chemical assessment could look like. DISCUSSION: Ontologies are an underexploited element of effective knowledge organization in the environmental health sciences. Agreeing on and implementing ontologies in chemical assessment is a complex but tractable process with four fundamental steps. Successful implementation of ontologies would not only make currently fragmented information about health risks from chemical exposures vastly more accessible, it could ultimately enable computational methods for chemical assessment that can take advantage of the full richness of data described in natural language in primary studies. https://doi.org/10.1289/EHP6994

Applying systematic review methods in chemical risk assessment

Context : Chemical risk assessment has traditionally been dependent on “narrative” approaches for synthesising evidence about potential health harms from exposure to chemical substances. However, narrative reviews are recognised as being vulnerable to a range of methodological shortcomings which introduce bias and inconsistency into the summarisation of scientific evidence. This is likely to be a contributing factor in a number of controversies about the safety of chemical substances. The potential value of systematic review methods for improving the transparency and validity of chemical risk assessments was arguably first articulated in the mid-2000s. By 2015, the first major frameworks for conducting systematic reviews of environmental health evidence had been published. What was not well understood at the time was how systematic review, as a technically exacting methodology originally developed for evaluating the effectiveness of interventions in healthcare, might be adapted to the specific workflows and evidence streams of chemical risk assessment. Objectives : The aim of this Thesis is to investigate how systematic review methods can be applied to the conduct of chemical risk assessment. This overall aim is broken down into four specific objectives: to identify practical challenges and knowledge gaps which impede the implementation of systematic review methods in chemical risk assessment; to define a consensus view on key recommended practices for the planning and conduct of systematic reviews in the environmental health sciences; to examine how “biological plausibility” as a concept fundamental to risk assessment is accommodated in systematic review methodologies; and to describe the role of ontologies in making evidence accessible for use in systematic chemical assessments. Discussion : The use of systematic review methods should improve the validity, utility and transparency of chemical risk assessments. However, the successful implementation of systematic review methods hinges on addressing a number of challenges, including the development of guidance for their conduct in environmental health contexts, and the technical development of methods where systematic review approaches need to be adapted to the specific requirements of chemical risk assessment. In terms of developing guidance, a detailed set of recommendations for the conduct of systematic reviews in environmental health and toxicological research was developed. These “COSTER” recommendations identify 70 practices across eight performance domains that will help ensure consistent and high standards for the growing number systematic reviews on environmental health topics. In terms of technical development of methods, “biological plausibility” is a concept used by risk assessors to describe the extent to which an experimental surrogate or knowledge of relevant biological mechanisms are informative of a systematic review conclusion. Through examination of 12 case examples it is concluded that “biological plausibility” is in fact already accommodated in the systematic review process under the assessment of the indirectness or external validity of evidence; however, the considerations which risk assessors take into account when assessing biological plausibility should be absorbed into the assessment of external validity of studies. Finally, examination of the concept of biological plausibility demonstrates the extreme heterogeneity and volume of data which has to be accommodated in chemical risk assessments. The role of ontologies in Knowledge Organisation Systems is examined as a key enabler of scaling up of systematic review methods to handling the volume of evidence which needs to be analysed if tens of thousands of chemicals, covering potentially millions of studies, are to be reviewed systematically