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Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.

ABSTRACT: Globalization of food networks increases opportunities for the spread of foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping of pathogens promises to vastly improve our ability to track and control foodborne disease, but to do so it must be combined with epidemiological, clinical, laboratory and other health care data (called "contextual data") to be meaningfully interpreted for regulatory and health interventions, outbreak investigation, and risk assessment. However, current multi-jurisdictional pathogen surveillance and investigation efforts are complicated by time-consuming data re-entry, curation and integration of contextual information owing to a lack of interoperable standards and inconsistent reporting. A solution to these challenges is the use of 'ontologies' - hierarchies of well-defined and standardized vocabularies interconnected by logical relationships. Terms are specified by universal IDs enabling integration into highly regulated areas and multi-sector sharing (e.g., food and water microbiology with the veterinary sector). Institution-specific terms can be mapped to a given standard at different levels of granularity, maximizing comparability of contextual information according to jurisdictional policies. Fit-for-purpose ontologies provide contextual information with the auditability required for food safety laboratory accreditation. Our research efforts include the development of a Genomic Epidemiology Ontology (GenEpiO), and Food Ontology (FoodOn) that harmonize important laboratory, clinical and epidemiological data fields, as well as existing food resources. These efforts are supported by a global consortium of researchers and stakeholders worldwide. Since foodborne diseases do not respect international borders, uptake of such vocabularies will be crucial for multi-jurisdictional interpretation of WGS results and data sharing.

SUBMITTER: Griffiths E

PROVIDER: S-EPMC5483436 | biostudies-other | 2017

REPOSITORIES: biostudies-other

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Project description:BACKGROUND:Wet markets are markets selling fresh meat and produce. Wet markets are critical for food security and sustainable development in their respective regions. Due to their cultural significance, they attract numerous visitors and consequently generate tourist-geared information on the Web (ie, on social networks such as TripAdvisor). These data can be used to create a novel, international wet market inventory to support epidemiological surveillance and control in such settings, which are often associated with negative health outcomes. OBJECTIVE:Using social network data, we aimed to assess the level of wet markets' touristic importance on the Web, produce the first distribution map of wet markets of touristic interest, and identify common diseases facing visitors in these settings. METHODS:A Google search was performed on 31 food market-related keywords, with the first 150 results for each keyword evaluated based on their relevance to tourism. Of all these queries, wet market had the highest number of tourism-related Google Search results; among these, TripAdvisor was the most frequently-occurring travel information aggregator, prompting its selection as the data source for this study. A Web scraping tool (ParseHub) was used to extract wet market names, locations, and reviews from TripAdvisor. The latter were searched for disease-related content, which enabled assignment of GeoSentinel diagnosis codes to each. This syndromic categorization was overlaid onto a mapping of wet market locations. Regional prevalence of the most commonly occurring symptom group - food poisoning - was then determined (ie, by dividing the number of wet markets per continent with more than or equal to 1 review containing this syndrome by the total number of wet markets on that continent with syndromic information). RESULTS:Of the 1090 hits on TripAdvisor for wet market, 36.06% (393/1090) conformed to the query's definition; wet markets were heterogeneously distributed: Asia concentrated 62.6% (246/393) of them, Europe 19.3% (76/393), North America 7.9% (31/393), Oceania 5.1% (20/393), Africa 3.1% (12/393), and South America 2.0% (8/393). Syndromic information was available for 14.5% (57/393) of wet markets. The most frequently occurring syndrome among visitors to these wet markets was food poisoning, accounting for 54% (51/95) of diagnoses. Cases of this syndrome were identified in 56% (22/39) of wet markets with syndromic information in Asia, 71% (5/7) in Europe, and 71% (5/7) in North America. All wet markets in South America and Oceania reported food poisoning cases, but the number of reviews with syndromic information was very limited in these regions (n=2). CONCLUSIONS:The map produced illustrates the potential role of touristically relevant social network data to support global epidemiological surveillance. This includes the possibility to approximate the global distribution of wet markets and to identify diseases (ie, food poisoning) that are most prevalent in such settings.

Project description:BackgroundMultisite clinical studies are increasingly using real-world data to gain real-world evidence. However, due to the heterogeneity of source data, it is difficult to analyze such data in a unified way across clinics. Therefore, the implementation of Extract-Transform-Load (ETL) or Extract-Load-Transform (ELT) processes for harmonizing local health data is necessary, in order to guarantee the data quality for research. However, the development of such processes is time-consuming and unsustainable. A promising way to ease this is the generalization of ETL/ELT processes.ObjectiveIn this work, we investigate existing possibilities for the development of generic ETL/ELT processes. Particularly, we focus on approaches with low development complexity by using descriptive metadata and structural metadata.MethodsWe conducted a literature review following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. We used 4 publication databases (ie, PubMed, IEEE Explore, Web of Science, and Biomed Center) to search for relevant publications from 2012 to 2022. The PRISMA flow was then visualized using an R-based tool (Evidence Synthesis Hackathon). All relevant contents of the publications were extracted into a spreadsheet for further analysis and visualization.ResultsRegarding the PRISMA guidelines, we included 33 publications in this literature review. All included publications were categorized into 7 different focus groups (ie, medicine, data warehouse, big data, industry, geoinformatics, archaeology, and military). Based on the extracted data, ontology-based and rule-based approaches were the 2 most used approaches in different thematic categories. Different approaches and tools were chosen to achieve different purposes within the use cases.ConclusionsOur literature review shows that using metadata-driven (MDD) approaches to develop an ETL/ELT process can serve different purposes in different thematic categories. The results show that it is promising to implement an ETL/ELT process by applying MDD approach to automate the data transformation from Fast Healthcare Interoperability Resources to Observational Medical Outcomes Partnership Common Data Model. However, the determining of an appropriate MDD approach and tool to implement such an ETL/ELT process remains a challenge. This is due to the lack of comprehensive insight into the characterizations of the MDD approaches presented in this study. Therefore, our next step is to evaluate the MDD approaches presented in this study and to determine the most appropriate MDD approaches and the way to integrate them into the ETL/ELT process. This could verify the ability of using MDD approaches to generalize the ETL process for harmonizing medical data.

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Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.

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