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      Ensembl 2019

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      Nucleic Acids Research
      Oxford University Press

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          Abstract

          The Ensembl project ( https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources. This year we describe our new and expanded gene, variant and comparative annotation capabilities, which led to a 50% increase in the number of vertebrate genomes we support. We have also doubled the number of available human variants and added regulatory regions for many mouse cell types and developmental stages. Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download.

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          Ensembl BioMarts: a hub for data retrieval across taxonomic space

          For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/
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            dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs.

            The purpose of the dbNSFP is to provide a one-stop resource for functional predictions and annotations for human nonsynonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome-sequencing study. A list of all potential nsSNVs and ssSNVs based on the human reference sequence were created and functional predictions and annotations were curated and compiled for each SNV. Here, we report a recent major update of the database to version 3.0. The SNV list has been rebuilt based on GENCODE 22 and currently the database includes 82,832,027 nsSNVs and ssSNVs. An attached database dbscSNV, which compiled all potential human SNVs within splicing consensus regions and their deleteriousness predictions, add another 15,030,459 potentially functional SNVs. Eleven prediction scores (MetaSVM, MetaLR, CADD, VEST3, PROVEAN, 4× fitCons, fathmm-MKL, and DANN) and allele frequencies from the UK10K cohorts and the Exome Aggregation Consortium (ExAC), among others, have been added. The original seven prediction scores in v2.0 (SIFT, 2× Polyphen2, LRT, MutationTaster, MutationAssessor, and FATHMM) as well as many SNV and gene functional annotations have been updated. dbNSFP v3.0 is freely available at http://sites.google.com/site/jpopgen/dbNSFP.
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              Earth BioGenome Project: Sequencing life for the future of life

              Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                08 January 2019
                08 November 2018
                08 November 2018
                : 47
                : Database issue , Database issue
                : D745-D751
                Affiliations
                European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Author notes
                To whom correspondence should be addressed. Tel: +44 1223 492581; Fax: +44 1223 494494; Email: flicek@ 123456ebi.ac.uk
                Author information
                http://orcid.org/0000-0002-7445-2419
                http://orcid.org/0000-0002-1119-6892
                http://orcid.org/0000-0002-2075-2387
                http://orcid.org/0000-0002-3894-4854
                http://orcid.org/0000-0002-1043-4756
                http://orcid.org/0000-0002-9009-4607
                http://orcid.org/0000-0001-8568-4306
                http://orcid.org/0000-0002-5394-8896
                http://orcid.org/0000-0002-4910-8202
                http://orcid.org/0000-0001-6452-5816
                http://orcid.org/0000-0002-0935-7271
                http://orcid.org/0000-0002-9475-4502
                http://orcid.org/0000-0002-7946-7062
                http://orcid.org/0000-0001-8843-3596
                http://orcid.org/0000-0002-4642-9043
                http://orcid.org/0000-0003-4894-7773
                http://orcid.org/0000-0003-3116-2558
                http://orcid.org/0000-0001-8491-9169
                http://orcid.org/0000-0002-9035-5301
                http://orcid.org/0000-0003-0967-3175
                http://orcid.org/0000-0002-2361-9530
                http://orcid.org/0000-0002-7669-2934
                http://orcid.org/0000-0003-3779-8581
                http://orcid.org/0000-0003-0247-3971
                http://orcid.org/0000-0003-0978-0309
                http://orcid.org/0000-0002-0918-4753
                http://orcid.org/0000-0002-8121-9797
                http://orcid.org/0000-0003-4789-7495
                http://orcid.org/0000-0001-9753-7995
                http://orcid.org/0000-0003-4422-5474
                http://orcid.org/0000-0003-2056-3946
                http://orcid.org/0000-0003-4341-2972
                http://orcid.org/0000-0002-0040-6591
                http://orcid.org/0000-0001-8683-7298
                http://orcid.org/0000-0001-6528-2633
                http://orcid.org/0000-0002-6575-5223
                http://orcid.org/0000-0002-4475-0183
                http://orcid.org/0000-0001-8858-5506
                http://orcid.org/0000-0002-8237-5660
                http://orcid.org/0000-0002-0215-0745
                http://orcid.org/0000-0001-5310-8830
                http://orcid.org/0000-0002-8350-1235
                http://orcid.org/0000-0002-1818-4050
                http://orcid.org/0000-0003-2799-3789
                http://orcid.org/0000-0002-1672-050X
                http://orcid.org/0000-0002-7860-3560
                http://orcid.org/0000-0003-0776-4428
                http://orcid.org/0000-0002-8386-1580
                http://orcid.org/0000-0002-7564-9125
                http://orcid.org/0000-0002-4862-3333
                http://orcid.org/0000-0002-3032-4095
                http://orcid.org/0000-0002-8886-4772
                http://orcid.org/0000-0001-5350-3056
                http://orcid.org/0000-0002-3897-7955
                Article
                gky1113
                10.1093/nar/gky1113
                6323964
                30407521
                d6e67a5c-5a59-4c18-82a9-33bd08415589
                © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 23 October 2018
                : 14 October 2018
                : 13 September 2018
                Page count
                Pages: 7
                Funding
                Funded by: Wellcome Trust 10.13039/100004440
                Award ID: WT108749/Z/15/Z
                Funded by: National Institutes of Health 10.13039/100000002
                Award ID: U41HG007823
                Award ID: 2U41HG007234
                Funded by: Biotechnology and Biological Sciences Research Council 10.13039/501100000268
                Award ID: BB/N019563/1
                Award ID: BB/M011615/1
                Funded by: Wellcome Trust 10.13039/100004440
                Award ID: WT108749/Z/15/A
                Award ID: WT104947/Z/14/Z
                Award ID: WT200990/Z/16/Z
                Award ID: WT201535/Z/16/Z
                Categories
                Database Issue

                Genetics
                Genetics

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