Tony Burdett
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View article: BioSamples database: the global hub for sample metadata and multi-omics integration
BioSamples database: the global hub for sample metadata and multi-omics integration Open
The BioSamples database (https://www.ebi.ac.uk/biosamples/) at the European Bioinformatics Institute (EMBL-EBI) is a core infrastructure resource that provides a centralized platform for the storage, curation, and dissemination of biologic…
View article: MorPhiC Consortium: towards functional characterization of all human genes
MorPhiC Consortium: towards functional characterization of all human genes Open
View article: Connecting ELIXIR communities and platforms
Connecting ELIXIR communities and platforms Open
View article: Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research
Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research Open
Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this…
View article: The European Nucleotide Archive in 2024
The European Nucleotide Archive in 2024 Open
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and acces…
View article: The international nucleotide sequence database collaboration (INSDC): enhancing global participation
The international nucleotide sequence database collaboration (INSDC): enhancing global participation Open
The members of the International Nucleotide Sequence Database Collaboration (INSDC; https://insdc.org) have built systems to collect, archive and disseminate sequence data for more than four decades. The three collaborating organizations, …
View article: Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses Open
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has ac…
View article: The future of data integration – Shaping ELIXIR’s interoperability platform with <i>real-world</i> use cases
The future of data integration – Shaping ELIXIR’s interoperability platform with <i>real-world</i> use cases Open
View article: Expression Atlas update: insights from sequencing data at both bulk and single cell level
Expression Atlas update: insights from sequencing data at both bulk and single cell level Open
Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI’s knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These …
View article: The European Nucleotide Archive in 2023
The European Nucleotide Archive in 2023 Open
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). The ENA is one of the three members of the International Nucleotide…
View article: PSII-6 Computational Tools and Resources for Analysis and Exploration of Single-Cell Rnaseq Data in Agriculture
PSII-6 Computational Tools and Resources for Analysis and Exploration of Single-Cell Rnaseq Data in Agriculture Open
The agriculture genomics community has numerous data submission standards available but little experience describing and storing single-cell (e.g., scRNAseq) data. Other single-cell genomics infrastructure efforts, such as the Human Cell A…
View article: The Translational Data Catalog - discoverable biomedical datasets
The Translational Data Catalog - discoverable biomedical datasets Open
View article: The FAIR Cookbook - the essential resource for and by FAIR doers
The FAIR Cookbook - the essential resource for and by FAIR doers Open
View article: FAIR in action - a flexible framework to guide FAIRification
FAIR in action - a flexible framework to guide FAIRification Open
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 framewor…
View article: Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses Open
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has ac…
View article: Toward a common standard for data and specimen provenance in life sciences
Toward a common standard for data and specimen provenance in life sciences Open
Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantl…
View article: FAIR in action - a flexible framework to guide FAIRification
FAIR in action - a flexible framework to guide FAIRification Open
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 framewor…
View article: MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues
MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues Open
View article: MGnify: the microbiome sequence data analysis resource in 2023
MGnify: the microbiome sequence data analysis resource in 2023 Open
The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The platform provides access to taxonomic assignments and functional annotations for ne…
View article: The European Nucleotide Archive in 2022
The European Nucleotide Archive in 2022 Open
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), offers those producing data an open and supported platform for the ma…
View article: The FAIR Cookbook - the essential resource for and by FAIR doers
The FAIR Cookbook - the essential resource for and by FAIR doers Open
Nowadays, the FAIR Principles guide data policy actions and professional practices in the public and private sectors. However, despite such global endorsements, the FAIR Principles are aspirational, remaining elusive at best, and intimidat…
View article: FAIR in action - a flexible framework to guide FAIRification
FAIR in action - a flexible framework to guide FAIRification Open
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 framewor…
View article: The Translational Data Catalog - discoverable biomedical datasets
The Translational Data Catalog - discoverable biomedical datasets Open
The discoverability of datasets resulting from the diverse range of translational and biomedical projects remains sporadic. It is especially difficult for datasets emerging from pre-competitive projects, often due to the legal constraints …
View article: The FAIR Cookbook - the essential resource for and by FAIR doers
The FAIR Cookbook - the essential resource for and by FAIR doers Open
Nowadays, the FAIR Principles guide data policy actions and professional practices in the public and private sectors. However, despite such global endorsements, the FAIR Principles are aspirational, remaining elusive at best, and intimidat…
View article: Toward a data infrastructure for the Plant Cell Atlas
Toward a data infrastructure for the Plant Cell Atlas Open
We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the Europea…
View article: From biomedical cloud platforms to microservices: next steps in FAIR data and analysis
From biomedical cloud platforms to microservices: next steps in FAIR data and analysis Open
View article: Community-driven ELIXIR activities in single-cell omics
Community-driven ELIXIR activities in single-cell omics Open
Single-cell omics (SCO) has revolutionized the way and the level of resolution by which life science research is conducted, not only impacting our understanding of fundamental cell biology but also providing novel solutions in cutting-edge…
View article: D3.6 Technical Feasibility Report
D3.6 Technical Feasibility Report Open
FAIRplus has produced four types of technical solutions: FAIRification processes, and adoption of a FAIRification framework FAIR assessment through adoption of the FAIR-DSM maturity model FAIR Cookbook and application of recipes FAIR tooli…
View article: D3.7 A FAIRification guidance tool for IMI
D3.7 A FAIRification guidance tool for IMI Open
The increased awareness and demand for FAIR data requires more FAIR guidelines and training. However, the FAIRplus squads’ collaboration with the IMI project shows that, despite the willingness to improve their projects, many project owner…
View article: D2.2 BYOD Guidelines
D2.2 BYOD Guidelines Open
Until now, there has been no standard or generalisable process for the ‘FAIRification’ of any given dataset. As a consequence, over the course of the FAIRplus project, it was necessary to develop such a methodology so that a) any given dat…