Towards a Common Standard for Data and Specimen Provenance in Life Sciences

The exchange of biological material and data has become an issue of major importance for research in biotechnology. At the same time, many reports indicate problems with quality, trustworthiness and reproducibility of research results, mainly due to poor documentation of data generation or collection of samples. Consequently, there is an urgent need for improved and standardized documentation of data and specimen used in research studies. In response to these issues, we are developing a provenance information standard for the biotechnology domain within the ISO Technical Committee 276 “Biotechnology”. The major objectives of the standard, now registered as ISO/WD 23494, are improved reproducibility of research results, enabling the assessment of the quality of biological samples and data, traceability and higher reliability of observations. We are convinced that the standardization project is of substantial interest to a broader audience, who we would also invite to comment and contribute to this comprehensive effort.Manuscript under consideration

EQRbot: A chatbot delivering EQR argument-based explanations

Data availability statement: The provided link: https://github.com/FCast07/EQRbot refers to the GitHub repository that stores the chatbot programming code.Recent years have witnessed the rise of several new argumentation-based support systems, especially in the healthcare industry. In the medical sector, it is imperative that the exchange of information occurs in a clear and accurate way, and this has to be reflected in any employed virtual systems. Argument Schemes and their critical questions represent well-suited formal tools for modeling such information and exchanges since they provide detailed templates for explanations to be delivered. This paper details the EQR argument scheme and deploys it to generate explanations for patients' treatment advice using a chatbot (EQRbot). The EQR scheme (devised as a pattern of Explanation-Question-Response interactions between agents) comprises multiple premises that can be interrogated to disclose additional data. The resulting explanations, obtained as instances of the employed argumentation reasoning engine and the EQR template, will then feed the conversational agent that will exhaustively convey the requested information and answers to follow-on users' queries as personalized Telegram messages. Comparisons with a previous baseline and existing argumentation-based chatbots illustrate the improvements yielded by EQRbot against similar conversational agents.This research was partially funded by the UK Engineering & Physical Sciences Research Council (EPSRC) under Grant #EP/P010105/1

EQRbot: A chatbot delivering EQR argument-based explanations

Recent years have witnessed the rise of several new argumentation-based support systems, especially in the healthcare industry. In the medical sector, it is imperative that the exchange of information occurs in a clear and accurate way, and this has to be reflected in any employed virtual systems. Argument Schemes and their critical questions represent well-suited formal tools for modeling such information and exchanges since they provide detailed templates for explanations to be delivered. This paper details the EQR argument scheme and deploys it to generate explanations for patients' treatment advice using a chatbot (EQRbot). The EQR scheme (devised as a pattern of Explanation-Question-Response interactions between agents) comprises multiple premises that can be interrogated to disclose additional data. The resulting explanations, obtained as instances of the employed argumentation reasoning engine and the EQR template, will then feed the conversational agent that will exhaustively convey the requested information and answers to follow-on users' queries as personalized Telegram messages. Comparisons with a previous baseline and existing argumentation-based chatbots illustrate the improvements yielded by EQRbot against similar conversational agents

Enhanced Version Control for Unconventional Applications

The Extensible Markup Language (XML) is widely used to store, retrieve, and share digital documents. Recently, a form of Version Control System has been applied to the language, resulting in Version-Aware XML allowing for enhanced portability and scalability. While Version Control Systems are able to keep track of changes made to documents, we think that there is untapped potential in the technology. In this dissertation, we present novel ways of using Version Control System to enhance the security and performance of existing applications. We present a framework to maintain integrity in offline XML documents and provide non-repudiation security features that are independent of central certificate repositories. In addition, we use Version Control information to enhance the performance of Automated Policy Enforcement eXchange framework (APEX), an existing document security framework developed by Hewlett-Packard (HP) Labs. Finally, we present an interactive and scalable visualization framework to represent Version-Aware-related data that helps users visualize and understand version control data, delete specific revisions of a document, and access a comprehensive overview of the entire versioning history

Linking provenance and its metadata in multi-organizational environments

Reproducibility issues are widely reported in life sciences. As a response, scientific communities have called for enhanced provenance information documenting the complete research life cycle, starting from biological or environmental material acquisition and ending with translating research results into practice. The integrity and trustworthiness of such provenance can be achieved by applying versioning mechanisms and cryptographic techniques, such as hashes or digital signatures, which are provenance metadata. However, the available provenance literature lacks an analysis of mechanisms for the exchange of provenance and its metadata between organizations as well as a grounded proposal of linking provenance and its metadata. In this work, we provide an in-depth analysis of the approaches for coupling provenance information and its metadata with documented research objects in the context of multi-organizational processes, leading to the categorization of possible approaches, description of their key properties, and derivation of requirements for underlying provenance models. We address the requirements by proposing a mechanism for linking provenance and its metadata by extending the Common Provenance Model, the open conceptual foundation for the ISO 23494 provenance standard series, currently under development. The concepts are demonstrated and validated on two complex use cases. This work is intended as a harmonized source of information on provenance coupling in the context of exchange of provenance between organizations, which can be used when designing or choosing a provenance solution. This type of usage is exemplified in the extension of the Common Provenance Model as another step toward a provenance standard for life sciences

A Review of Significant European Foodborne Outbreaks in the Last Decade.

ABSTRACT Foodborne diseases remain a global public health challenge worldwide. The European surveillance system of multistate foodborne outbreaks integrates elements from public and animal health and the food chain for early detection, assessment, and control. This review includes descriptions of the significant outbreaks that occurred in Europe in the last decade. Their significance and relevance to public health is derived from the changes, improvements, and novelties that pushed toward building a safer food system in the European Union, certainly driven by the One Health approach. In 2011, a point source monoclonal outbreak of infections caused by Escherichia coli serotype O104:H4 in sprouted seeds resulted in hundreds of cases of hemolytic uremic syndrome and several fatalities. In 2015, a prolonged outbreak of Listeria monocytogenes infections caused by contamination of frozen corn in Europe resulted in 47 cases and nine deaths. In 2016, a persistent polyclonal outbreak of Salmonella Enteritidis was linked to the consumption of eggs and was associated with hundreds of cases. The outbreak evaluations highlight the importance of rapid sharing of data (e.g., sequencing and tracing data) and the need for harmonizing bioinformatics outputs and computational approaches to facilitate detection and investigation of foodborne illnesses. These outbreaks led to development of a legal framework for a European collaboration platform for sharing whole genome sequence data and enabled the enforcement of existing hygiene and food safety provisions and the development of new hygiene guidelines and best practices. This review also briefly touches on the new trends in information technologies that are being explored for food traceability and safety. These technologies could enhance the traceability of food throughout the supply chain and redirect the conventional tracing system toward a digitized supply chain. HIGHLIGHT