EBI Metagenomics

EBI Metagenomics
Name	EBI Metagenomics
Type	Bioinformatics resource
Founded	2010
Owner	European Bioinformatics Institute
Location	Hinxton

EBI Metagenomics is a bioinformatics platform maintained by the European Bioinformatics Institute that provided large-scale analysis of environmental sequence data from metagenomic and metatranscriptomic projects. The resource integrated pipelines for taxonomic classification and functional annotation to support researchers associated with institutions such as the Wellcome Trust Sanger Institute, European Molecular Biology Laboratory, National Institutes of Health, Joint Genome Institute, and Broad Institute. It served communities working on projects like the Human Microbiome Project, Tara Oceans Expedition, Earth Microbiome Project, and collaborations with the Genome Reference Consortium and the European Nucleotide Archive.

Overview

EBI Metagenomics functioned as a service to process raw reads and assemblies submitted through portals like the European Nucleotide Archive and linked outputs to resources such as the UniProt and InterPro knowledgebases. The resource supported data standards promoted by organizations including the Genomic Standards Consortium, the International Nucleotide Sequence Database Collaboration, and the Global Biodiversity Information Facility. By interfacing with analytical frameworks from groups such as the European Bioinformatics Institute and the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), it enabled integration with reference resources maintained by teams at UniProt Consortium, Pfam Consortium, and the Gene Ontology Consortium.

History and Development

Development began in the early 2010s with funding and coordination involving stakeholders such as the Wellcome Trust, the European Commission, and national funding bodies including the Biotechnology and Biological Sciences Research Council. The platform evolved in parallel with projects like the Human Microbiome Project and the Tara Oceans Expedition, adopting methods influenced by pipelines from the Joint Genome Institute and software from teams at the Broad Institute, Argonne National Laboratory, and the European Molecular Biology Laboratory. Key milestones included integration with the European Nucleotide Archive for submission workflows, adoption of annotation databases maintained by UniProt, InterPro, Pfam, and enhancements driven by collaborations with the Genomic Standards Consortium and researchers from institutions such as University of Cambridge and Wellcome Sanger Institute.

Data Submission and Processing Pipeline

Submitters routed metagenomic and metatranscriptomic sequence data to EBI Metagenomics through channels coordinated with the European Nucleotide Archive and project portals linked to initiatives like the Earth Microbiome Project and the Human Microbiome Project. The pipeline incorporated preprocessing and quality control steps using tools and formats promoted by the Open Bioinformatics Foundation and software originating from teams at the European Molecular Biology Laboratory, Wellcome Sanger Institute, and Broad Institute. Read trimming, assembly, and gene prediction steps connected to reference collections such as UniProtKB, InterPro, Pfam, and the Gene Ontology Consortium to enable downstream annotation consistent with community standards advocated by the Genomic Standards Consortium and the International Nucleotide Sequence Database Collaboration.

Functional and Taxonomic Analysis

Taxonomic classification in the platform relied on marker-based and whole-read approaches informed by reference sets curated by the SILVA consortium, the Greengenes project, and sequence resources at the European Nucleotide Archive, while functional annotation mapped predicted proteins to databases such as UniProt, InterPro, Pfam, TIGRFAMs, and ontologies from the Gene Ontology Consortium. The workflow produced outputs interpretable by comparative projects including the Human Microbiome Project, the Earth Microbiome Project, and the Tara Oceans Expedition, and supported metaanalysis by integrating with community resources such as the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) toolkits and datasets from the Joint Genome Institute.

Data Access and Visualization Tools

Processed datasets were exposed through web interfaces and programmatic APIs interoperable with platforms operated by the European Bioinformatics Institute, the European Nucleotide Archive, and the UniProt Consortium. Visualization and exploration capabilities leveraged standards and tools from projects like the Galaxy Project, the InterPro Consortium, and visualization libraries used by teams at the Wellcome Trust Sanger Institute and the European Molecular Biology Laboratory. Outputs were designed to be compatible with downstream analysis in environments provided by organizations such as the Joint Genome Institute, the Broad Institute, and national infrastructures including the European Open Science Cloud.

Applications and Impact

The platform supported diverse applications spanning environmental monitoring programs run by agencies like the European Environment Agency, human health studies aligned with the Human Microbiome Project, oceanographic research linked to the Tara Oceans Expedition, and agricultural microbiome initiatives involving institutions such as Rothamsted Research and universities including the University of Oxford and University of Cambridge. By harmonizing annotation with databases maintained by the UniProt Consortium, the InterPro Consortium, and the Gene Ontology Consortium, it enabled comparative studies cited alongside work from the Joint Genome Institute, the Broad Institute, and funding programs administered by the Wellcome Trust and the European Commission.

Category:Bioinformatics resources