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      UniProt: a worldwide hub of protein knowledge

      research-article
      Author(s): The UniProt Consortium 1 , 2 , 3 , 4
      Publication date (Electronic):
      Journal: Nucleic Acids Research
      Publisher: Oxford University Press

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          Abstract

          The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins. These annotations are supplemented by annotations provided by rule based automated systems, and those imported from other resources. In this article we describe significant updates that we have made over the last 2 years to the resource. We have greatly expanded the number of Reference Proteomes that we provide and in particular we have focussed on improving the number of viral Reference Proteomes. The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

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          A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

          Jianzhao Liu, Yanan Yue, Dali Han … (2013)
          N 6-methyladenosine (m6A) is the most prevalent and reversible internal modification in mammalian messenger and non-coding RNAs. We report here that human METTL14 catalyzes m6A RNA methylation. Together with METTL3, the only previously known m6A methyltransferase, these two proteins form a stable heterodimer core complex of METTL3-14 that functions in cellular m6A deposition on mammalian nuclear RNAs. WTAP, a mammalian splicing factor, can interact with this complex and affect this methylation.
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            UniProt: the universal protein knowledgebase

            (2016)
            The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically review experimental and predicted data for each protein. The remainder are automatically annotated based on rule systems that rely on the expert curated knowledge. Since our last update in 2014, we have more than doubled the number of reference proteomes to 5631, giving a greater coverage of taxonomic diversity. We implemented a pipeline to remove redundant highly similar proteomes that were causing excessive redundancy in UniProt. The initial run of this pipeline reduced the number of sequences in UniProt by 47 million. For our users interested in the accessory proteomes, we have made available sets of pan proteome sequences that cover the diversity of sequences for each species that is found in its strains and sub-strains. To help interpretation of genomic variants, we provide tracks of detailed protein information for the major genome browsers. We provide a SPARQL endpoint that allows complex queries of the more than 22 billion triples of data in UniProt (http://sparql.uniprot.org/). UniProt resources can be accessed via the website at http://www.uniprot.org/.
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              Ensembl 2018

              Daniel Zerbino, Premanand Achuthan, Wasiu Akanni … (2017)
              Abstract The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 08 January 2019
                Publication date (Electronic): 05 November 2018
                Publication date PMC-release: 05 November 2018
                Volume: 47
                Issue: Database issue , Database issue
                Pages: D506-D515
                Affiliations
                [1 ]European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                [2 ]SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland
                [3 ]Protein Information Resource, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC 20007, USA
                [4 ]Protein Information Resource, University of Delaware, 15 Innovation Way, Suite 205, Newark DE 19711, USA
                Author notes
                To whom correspondence should be addressed. Tel: +44 1223 494 100; Fax: +44 1223 494 468; Email: agb@ 123456ebi.ac.uk

                Present address: Alex Bateman, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

                Article
                Publisher ID: gky1049
                DOI: 10.1093/nar/gky1049
                PMC ID: 6323992
                PubMed ID: 30395287
                SO-VID: 42fd9466-139a-4a99-a103-bda97c18ecf3
                Copyright © © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                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
                Date accepted : 18 October 2018
                Date revision received : 15 October 2018
                Date received : 14 September 2018
                Page count
                Pages: 10
                Funding
                Funded by: National Institutes of Health 10.13039/100000002
                Award ID: U24HG007822
                Funded by: National Human Genome Research Institute 10.13039/100000051
                Award ID: U41HG007822
                Award ID: U41HG002273
                Funded by: National Institute of General Medical Sciences 10.13039/100000057
                Award ID: R01GM080646
                Award ID: P20GM103446
                Award ID: U01GM120953
                Funded by: Biotechnology and Biological Sciences Research Council 10.13039/501100000268
                Award ID: BB/M011674/1
                Funded by: British Heart Foundation 10.13039/501100000274
                Award ID: RG/13/5/30112
                Categories
                Subject: Database Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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