A5006394765- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Scientific Computing and Data Management
- Data-Driven Disease Surveillance
- Nutrition, Genetics, and Disease
- Antibiotic Resistance in Bacteria
- Research Data Management Practices
- Bioinformatics and Genomic Networks
- Zoonotic diseases and public health
- Genomics and Phylogenetic Studies
- Pharmaceutical and Antibiotic Environmental Impacts
- Identification and Quantification in Food
- Genomics and Rare Diseases
- Health disparities and outcomes
- Advanced Chemical Sensor Technologies
- Plant tissue culture and regeneration
- Art Therapy and Mental Health
- Bacterial Identification and Susceptibility Testing
- Culinary Culture and Tourism
- Microbial infections and disease research
- Ethics in Clinical Research
- Gut microbiota and health
- Topic Modeling
- Food Supply Chain Traceability
- Transgenic Plants and Applications
Simon Fraser University
2021-2025
University of British Columbia
2015-2022
Bridge University
2022
BC Centre for Disease Control
2017
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses high-quality data sequences within controlled vocabulary, Ontology (ARO), designed by biocuration team to integrate with software development efforts for resistome analysis prediction, such as CARD's Gene Identifier (RGI)...
Abstract The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation interpretation of resistomes. As version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, 5057 detection models that can be used by accompanying Gene Identifier (RGI) software annotate genomic or...
The construction of high capacity data sharing networks to support increasing government and commercial exchange has highlighted a key roadblock: the content existing Internet-connected information remains siloed due multiplicity local languages dictionaries. This lack digital lingua franca is obvious in domain human food as materials travel from their wild or farm origin, through processing distribution chains, consumers. Well defined, hierarchical vocabulary, connected with logical...
Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple can be problematic, as they developed independently, which lead incompatibilities. The Open Biomedical Ontologies (OBO) Foundry was created address by facilitating development, harmonization, application sharing ontologies, guided set overarching principles. One challenge in reaching these...
Abstract Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools resources, advocate greater openness, interoperability, accessibility, reproducibility in public health microbial bioinformatics. In face current pandemic, PHA4GE has identified need fit-for-purpose, open-source SARS-CoV-2...
Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge an accurate computable form. However, their construction maintenance demand substantial resources necessitate collaboration between domain experts, curators, ontology experts. We present Dynamic Retrieval Augmented Generation using AI (DRAGON-AI), generation method employing Large Language Models (LLMs) (RAG). DRAGON-AI can...
Abstract Whole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods. Implementation of WGS in routine microbiology laboratories impeded by lack user-friendly automated semi-automated pipelines, restrictive jurisdictional data sharing policies, the proliferation non-interoperable analytical reporting systems. To address these issues, we...
Globalization of food networks increases opportunities for the spread foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping promises to vastly improve our ability track control disease, but do so it must be combined with epidemiological, clinical, laboratory other health care data (called "contextual data") meaningfully interpreted regulatory interventions, outbreak investigation, risk assessment. However, current multi-jurisdictional...
The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase (intI) play a key role in alterations microbial communities spread environment. In order to assess effect activities on watersheds southwestern British Columbia, presence putative was analyzed microbiome agricultural, urban influenced, protected watersheds....
The Canadian Genomics Research and Development Initiative for Antimicrobial Resistance (GRDI-AMR) uses a genomics-based approach to understand how health care, food production the environment contribute development of antimicrobial resistance. Integrating genomics contextual data streams across One Health continuum is challenging because diversity in scope, content structure. To better enable harmonization analyses, standard was developed. However, standards does not guarantee their use....
As viruses evolve, they accumulate genetic mutations that can influence disease severity, transmissibility, and the effectiveness of vaccines therapeutics. Real-time tracking viral their functional impacts is essential to understand these changes assess implications for public health responses. VIRUS-MVP an interactive, portable platform designed comprehensive surveillance mutations. Initially developed SARS-CoV-2, it now fully supports mpox expanding include influenza RSV. The links...
Huge advances in peer-to-peer systems and attempts to develop the semantic web have revealed a critical issue information across multiple domains: absence of interoperability. Today, businesses operating digital environment require increased supply-chain automation, interoperability, data governance. While research on interoperability has recently received much attention, dearth studies investigates relationship between these two concepts depth. To address this knowledge gap, objective study...
The regular analysis of whole-genome sequence data in collections such as NCBI’s Pathogen Detection Database is used by many public health organizations to detect outbreaks infectious disease. However, isolate metadata these databases are often incomplete and poor quality.
Informed policy and decision-making for food systems, nutritional security, global health would benefit from standardization comparison of composition data, spanning production to consumption. To address this challenge, we present a formal controlled vocabulary terms, definitions, relationships within the Compositional Dietary Nutrition Ontology (CDNO, www.cdno.info) that enables description attributes material entities contributing human diet. We demonstrate how ongoing community...
Since its creation in 2016, the FoodOn food ontology has become an interconnected partner various academic and government projects that span agricultural public health domains. This paper examines recent data interoperability capabilities arising from food-related ontologies belonging to, or compatible with, encyclopedic Open Biological Biomedical Ontology Foundry (OBO) platform, how research organizations industry might utilize them for their own exchange. Projects are seeking standardized...
As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, optimization wet- dry-lab procedures. Achieving these goals algorithms, pipelines instruments often requires that lower quality datasets be made available analysis comparison alongside those higher quality. This range data in reference sets can complicate sharing sub-optimal are vital community reproducibility...
Abstract Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple can be problematic, as they developed independently, which lead incompatibilities. The Open Biomedical Ontologies (OBO) Foundry was created address by facilitating development, harmonization, application, sharing ontologies, guided set overarching principles. One challenge in...
Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well research. In order to make use of pathogen data, they must be interpreted using contextual data (metadata). Contextual include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how information captured by different authorities it encoded databases poses challenges interpretation,...
Globally, present regulations treat pesticide use with a light touch, leaving users scarce reporting requirements in the field. However, numerous initiatives have been undertaken to reduce risks from product and provide public sufficient information. Nevertheless, food chain actors are not required disclose much information on hazards, many undervalued safety aspects. This situation has resulted gaps concerning production, authorization, use, impact of products for both consumers regulatory...
People often value the sensual, celebratory, and health aspects of food, but behind this experience exists many other value-laden agricultural production, distribution, manufacturing, physiological processes that support or undermine a healthy population sustainable future. The complexity such is evident in both every-day food preparation recipes industrial packaging storage, each which depends critically on human machine agents, chemical organismal ingredient references, explicit...
Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations, as well research. In order to make use of pathogen data, it must be interpreted using contextual data (metadata). Contextual includes sample metadata, laboratory methods, patient demographics, clinical outcomes, and epidemiological information. However, the variability in how information captured by different authorities encoded databases poses challenges interpretation,...
We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, O157. also draft assemblies, with standardized metadata, 360 STEC isolated watersheds, animals, farms, food, infections.