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1.
Nucleic Acids Res ; 52(D1): D92-D97, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37956313

RESUMEN

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 Sequence Database Collaboration (INSDC). It serves the bioinformatics community worldwide via the submission, processing, archiving and dissemination of sequence data. The ENA supports data types ranging from raw reads, through alignments and assemblies to functional annotation. The data is enriched with contextual information relating to samples and experimental configurations. In this article, we describe recent progress and improvements to ENA services. In particular, we focus upon three areas of work in 2023: FAIRness of ENA data, pandemic preparedness and foundational technology. For FAIRness, we have introduced minimal requirements for spatiotemporal annotation, created a metadata-based classification system, incorporated third party metadata curations with archived records, and developed a new rapid visualisation platform, the ENA Notebooks. For foundational enhancements, we have improved the INSDC data exchange and synchronisation pipelines, and invested in site reliability engineering for ENA infrastructure. In order to support genomic surveillance efforts, we have continued to provide ENA services in support of SARS-CoV-2 data mobilisation and have adapted these for broader pathogen surveillance efforts.


Asunto(s)
Genómica , Nucleótidos , Biología Computacional , Bases de Datos de Ácidos Nucleicos , Internet , Reproducibilidad de los Resultados , Europa (Continente)
2.
Nucleic Acids Res ; 51(D1): D753-D759, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36477304

RESUMEN

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 nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets, which are derived from a wide range of different environments. Over the past 3 years, MGnify has not only grown in terms of the number of datasets contained but also increased the breadth of analyses provided, such as the analysis of long-read sequences. The MGnify protein database now exceeds 2.4 billion non-redundant sequences predicted from metagenomic assemblies. This collection is now organised into a relational database making it possible to understand the genomic context of the protein through navigation back to the source assembly and sample metadata, marking a major improvement. To extend beyond the functional annotations already provided in MGnify, we have applied deep learning-based annotation methods. The technology underlying MGnify's Application Programming Interface (API) and website has been upgraded, and we have enabled the ability to perform downstream analysis of the MGnify data through the introduction of a coupled Jupyter Lab environment.


Asunto(s)
Microbiota , Análisis de Secuencia , Genómica/métodos , Metagenoma , Metagenómica/métodos , Microbiota/genética , Programas Informáticos , Análisis de Secuencia/métodos
3.
Nucleic Acids Res ; 51(D1): D121-D125, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36399492

RESUMEN

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 management, archiving, publication, and dissemination of data; and to the scientific community as a whole, it offers a globally comprehensive data set through a host of data discovery and retrieval tools. Here, we describe recent updates to the ENA's submission and retrieval services as well as focused efforts to improve connectivity, reusability, and interoperability of ENA data and metadata.


Asunto(s)
Bases de Datos de Ácidos Nucleicos , Academias e Institutos , Biología Computacional , Internet , Programas Informáticos , Conjuntos de Datos como Asunto
4.
Nucleic Acids Res ; 50(D1): D106-D110, 2022 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-34850158

RESUMEN

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 access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Here, we outline the major updates to ENA's services and infrastructure that have been delivered over the past year.


Asunto(s)
Biología Computacional , Bases de Datos de Ácidos Nucleicos , Nucleótidos/genética , Programas Informáticos , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Internet , Anotación de Secuencia Molecular , Nucleótidos/clasificación
5.
Nucleic Acids Res ; 49(D1): D82-D85, 2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33175160

RESUMEN

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scientific community and for the acceleration of the global research effort. Here we highlight the major developments to ENA services and content in 2020, focussing in particular on the recently released updated ENA browser, modernisation of our release process and our data coordination collaborations with specific research communities.


Asunto(s)
Biología Computacional/métodos , Bases de Datos de Ácidos Nucleicos/tendencias , Ácidos Nucleicos/genética , Nucleótidos/genética , Bases de Datos de Ácidos Nucleicos/estadística & datos numéricos , Europa (Continente) , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Internet , Anotación de Secuencia Molecular , Ácidos Nucleicos/química , Nucleótidos/química , Análisis de Secuencia de ADN , Análisis de Secuencia de ARN
6.
Nucleic Acids Res ; 48(D1): D570-D578, 2020 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-31696235

RESUMEN

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.


Asunto(s)
Metagenoma , Microbiota , Filogenia , Programas Informáticos , Archaea/clasificación , Archaea/genética , Bacterias/clasificación , Bacterias/genética , ADN Espaciador Ribosómico/genética , Bases de Datos Genéticas , Metagenómica/métodos
7.
Nucleic Acids Res ; 48(D1): D70-D76, 2020 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-31722421

RESUMEN

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory's European Bioinformatics Institute provides open and freely available data deposition and access services across the spectrum of nucleotide sequence data types. Making the world's public sequencing datasets available to the scientific community, the ENA represents a globally comprehensive nucleotide sequence resource. Here, we outline ENA services and content in 2019 and provide an insight into selected key areas of development in this period.


Asunto(s)
Biología Computacional , Bases de Datos de Ácidos Nucleicos , Genómica , Biología Computacional/métodos , Europa (Continente) , Genómica/métodos , Anotación de Secuencia Molecular , Programas Informáticos , Interfaz Usuario-Computador , Navegador Web
8.
Bioinformatics ; 35(15): 2671-2673, 2019 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-30535283

RESUMEN

SUMMARY: Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the assembly to a genomic map. However, currently, tools for visualization are limited to use on a Windows operating system or are developed initially for visualizing large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualize and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments. It provides a fast, simple alternative to the large optical mapping analysis programs currently available for this area of research. AVAILABILITY AND IMPLEMENTATION: MapOptics is implemented in Java 1.8 and released under an MIT licence. MapOptics can be downloaded from https://github.com/FadyMohareb/mapoptics and run on any standard desktop computer equipped with a Java Virtual Machine (JVM). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Programas Informáticos , Mapeo Cromosómico , Genómica , Mapeo Restrictivo , Análisis de Secuencia de ADN
9.
J Mol Biol ; 435(14): 168016, 2023 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-36806692

RESUMEN

An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues. Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.


Asunto(s)
Genoma Microbiano , Metagenoma , Metagenoma/genética , Metagenómica
10.
F1000Res ; 122023.
Artículo en Inglés | MEDLINE | ID: mdl-38882711

RESUMEN

Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth's biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.


Asunto(s)
Biodiversidad , Humanos , Conservación de los Recursos Naturales
11.
Wellcome Open Res ; 7: 279, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-39091415

RESUMEN

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

12.
mSystems ; 6(1)2021 02 23.
Artículo en Inglés | MEDLINE | ID: mdl-33622857

RESUMEN

Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community. To understand how these standards are being adopted, or the barriers to adoption, across research domains, institutions, and funding agencies, the National Microbiome Data Collaborative (NMDC) hosted a workshop in October 2019. This report provides a summary of discussions that took place throughout the workshop, as well as outcomes of the working groups initiated at the workshop.

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