Mélanie Courtot
A5008255694- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Semantic Web and Ontologies
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Ethics in Clinical Research
- vaccines and immunoinformatics approaches
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Cancer Genomics and Diagnostics
- Computational Drug Discovery Methods
- Geological Modeling and Analysis
- Service-Oriented Architecture and Web Services
- SARS-CoV-2 and COVID-19 Research
- Cell Image Analysis Techniques
- Influenza Virus Research Studies
- Single-cell and spatial transcriptomics
- Natural Language Processing Techniques
- Pharmacovigilance and Adverse Drug Reactions
- Childhood Cancer Survivors' Quality of Life
- Delphi Technique in Research
- Gene expression and cancer classification
Ontario Institute for Cancer Research
2022-2024
University of Toronto
2023-2024
European Bioinformatics Institute
2016-2023
Wellcome Trust
2016-2021
Terry Fox Research Institute
2009-2020
Simon Fraser University
2014-2016
Bioinformatics Institute
2015
Fred Hutch Cancer Center
2014
Stanford University
2014
National Institutes of Health
2014
The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis genes, proteins and mutations involved in AMR. CARD ontologically structured, model centric, spans breadth AMR drug classes mechanisms, including intrinsic, mutation-driven acquired resistance. It built upon Ontology (ARO), custom built, interconnected hierarchical...
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
The FAIR principles have been widely cited, endorsed and adopted by a broad range of stakeholders since their publication in 2016. By intention, the 15 guiding do not dictate specific technological implementations, but provide guidance for improving Findability, Accessibility, Interoperability Reusability digital resources. This has likely contributed to adoption principles, because individual stakeholder communities can implement own solutions. However, it also resulted inconsistent...
Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange information retrieval.
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack community-wide, consensus-based, human- machine-interpretable language for describing phenotypes genomic environmental contexts is perhaps most pressing scientific bottleneck integration across many key fields in biology, including genomics, systems development, medicine, evolution, ecology, systematics. Here we survey phenomics...
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical genomic data through both harmonized aggregation federated approaches. decreasing cost sequencing (along with other genome-wide molecular assays) increasing evidence its utility will soon drive generation sequence from tens millions humans, levels diversity. In this perspective, we present GA4GH strategies addressing major challenges revolution. We...
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 The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good stewardship prerequisite reproducibility. Nowadays, guides policy actions professional practices in public private sectors. Despite such endorsements, however, Principles are aspirational, remaining elusive at best, intimidating worst. To address lack of practical guidance, help with capability gaps, we developed Cookbook, an open,...
Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, OBO Foundry principles require that these ontologies be open non-redundant, avoiding duplication terms through re-use existing resources. As current options to do so present various difficulties, new approach, MIREOT, allows specifying import single terms. Initial implementations allow for controlled selected annotations...
While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this is not always suitable. Current editing tools present challenges for working with large ontologies and direct OWL imports can prove impractical day-to
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information Description Frameworks (RDFs) HTTP. Ontologies, which logically represent relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology server that stores RDF triple store technology supports query, visualization linkage terms. also default for publishing browsing biomedical ontologies Open Biological...
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present world's public sequencing data benefit of entire scientific community acceleration global research effort. Here we highlight major developments ENA services content 2020, focussing particular on recently released updated browser, modernisation our release process...
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers a core component this infrastructure. Drawing our experience work by other groups, we outline 10 lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose actions...
Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive was often highly acidic and mixed with heavy metals, has been leaking into environment since 1950s. Because danger expense cleanup such sites by physicochemical processes, in situ bioremediation methods are being developed for contaminated ground groundwater. To date, most microbial treatment proposed high-level employs radiation-resistant...
Abstract The BioSamples database at EMBL-EBI is the central institutional repository for sample metadata storage and connection to archives other resources. technical improvements our infrastructure described in last update have enabled us scale accommodate an increasing number of communities, resulting a higher submissions more heterogeneous data. now has valuable set features processes improve data quality BioSamples, particular enriching content following FAIR principles. In this...
Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they processed made available comply with ethical regulatory frameworks informed consent data conditions. To enable streamline access these datasets, the Global Alliance Genomics Health (GA4GH) Data Use Researcher Identities (DURI) work stream developed approved...
The COVID-19 pandemic has highlighted the need for FAIR (Findable, Accessible, Interoperable, and Reusable) data more than any other scientific challenge to date. We developed a flexible, multi-level, domain-agnostic FAIRification framework, providing practical guidance improve FAIRness both existing future clinical molecular datasets. validated framework in collaboration with several major public-private partnership projects, demonstrating delivering improvements across all aspects of...
The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other resources. has recently undergone major changes, both in terms of data content supporting infrastructure. more than doubled from around 2 million samples 2014 just over 5 2018. Fast, reciprocal exchange was fully established between sister Biosample databases INSDC partners, enabling worldwide common representation centralization metadata. platform been upgraded accommodate anticipated...
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...
Bio-ontologies typically require multiple axes of classification to support the needs their users. Development such ontologies can only be made scalable and sustainable by use inference automate via consistent patterns axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These need documented a form that requires minimal expertise understand edit validated applied using any various programmatic approaches working with ontologies. Here we describe system, Dead...