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Please note that we have no fixed timeline for most of these items New datasets and scaling-up for large data expansion Expanding…" /> <meta property="article:published_time" content="2011-02-17T13:03:32+00:00" /> <meta property="article:modified_time" content="2021-04-14T10:40:56+00:00" /> <meta property="og:site_name" content="Ensembl Blog" /> <meta property="og:image" content="https://www.ensembl.info/wp-content/uploads/2018/01/cropped-ebang-512.png" /> <meta property="og:image:width" content="512" /> <meta property="og:image:height" content="512" /> <meta property="og:image:alt" content="" /> <meta property="og:locale" content="en_GB" /> <meta name="twitter:text:title" content="Future Plans" /> <meta name="twitter:image" content="https://www.ensembl.info/wp-content/uploads/2018/01/cropped-ebang-512-270x270.png" /> <meta name="twitter:card" content="summary" />  <link rel="icon" href="https://www.ensembl.info/wp-content/uploads/2018/01/cropped-ebang-512-32x32.png" sizes="32x32" /> 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By using the site you are agreeing to this as outlined in our <a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice" rel=""> Privacy Policy </a> </div> </aside> </div> </div> </div> <div id="primary" class="content-area col-lg-9" itemprop="mainContentOfPage"> <div itemscope itemtype="http://schema.org/Article" id="content" class="site-content" role="main"> <article id="post-524" class="post-524 page type-page status-publish hentry"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Future Plans</h1> </header> <div class="entry-content" itemprop="articleBody"> <p>The following updates are planned for upcoming releases of Ensembl.</p> <p><strong>Please note that we have no fixed timeline for most of these items</strong></p> <h2><b>New datasets and scaling-up for large data expansion</b></h2> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Expanding Ensembl </span><a href="http://www.ensembl.info/2020/06/25/ensembl-rapid-release/" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">Rapid Release</span></a> <a href="http://rapid.ensembl.org" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">website</span></a><span style="font-weight: 400;"> allowing faster annotation and deployment of new species in a two weeks release cycle:</span> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Adding REST server</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Adding homologue data and possibly pairwise alignments</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Adding Ensembl VEP</span></li> </ul> </li> <li style="font-weight: 400;"><span style="font-weight: 400;">Expanding the breath of species with annotation and comparative analyses to </span><a href="http://www.ensembl.info/2019/03/15/genomics-gets-global-ensembl-and-the-vgp/" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">Vertebrate Genomes Project</span></a><span style="font-weight: 400;"> (</span><a href="https://vertebrategenomesproject.org/" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">VGP</span></a><span style="font-weight: 400;">) and <a href="http://projects.ensembl.org/darwin-tree-of-life/" target="_blank" rel="noopener noreferrer">Darwin Tree of Life</a> (</span><a href="https://www.darwintreeoflife.org/" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">DToL</span></a><span style="font-weight: 400;">):</span> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Scaling-up the gene tree pipeline</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Implementing Cactus as a scalable multiple genome aligner</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Annotating non-vertebrate eukaryotes as part of DToL</span></li> </ul> </li> <li style="font-weight: 400;"><span style="font-weight: 400;">Expanding the depth of our annotation of farmed animals and other species with high socio-economic value using transcriptomic data, Nanopore, IsoSeq, etc.</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Defining community-based comparative species sets, e.g. farm animals, crops, VGP</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Expanding multiple assemblies and comparative analysis within single species: breeds, strains, cultivars, ecotypes and haplotypes</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Extending the regulatory build to species in the Functional Annotation of Animal Genomes (</span><a href="https://www.animalgenome.org/community/FAANG/index" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">FAANG</span></a><span style="font-weight: 400;">) Consortium</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Capturing gene-gene interactions between microorganisms and host species in microbiomes and disease and presenting them in Ensembl, starting with gene-gene interactions from </span><a href="http://www.phi-base.org/" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">PHI-base</span></a></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Enabling </span><a href="https://www.ebi.ac.uk/eva/" target="_blank" rel="noopener noreferrer"><span style="font-weight: 400;">EVA</span></a><span style="font-weight: 400;">-driven variation viewing on microbial species, starting with </span><i><span style="font-weight: 400;">Plasmodium falciparum</span></i><span style="font-weight: 400;">, </span><i><span style="font-weight: 400;">Zymoseptoria tritici</span></i><span style="font-weight: 400;">, </span><i><span style="font-weight: 400;">Botrytis cinerea</span></i><span style="font-weight: 400;">, </span><i><span style="font-weight: 400;">S. cerevisiae</span></i><span style="font-weight: 400;"> and </span><i><span style="font-weight: 400;">S. pombe</span></i></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Update of crop reference genomes, their cultivars and annotation focusing on wheat (IWGSCv2.0), rice, maize, </span><i><span style="font-weight: 400;">Sorghum</span></i><span style="font-weight: 400;"> and grapevines</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">New library of repeated elements in plant genomes</span></li> </ul> <h2><b>New Ensembl website</b></h2> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">First public release MAP (minimal acceptable product):</span> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Automated species processing to enable first seven species</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Multiple transcripts on genome browser</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Displays for summary and functional information of genes and transcripts</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Search</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Help documentation</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Landing pages for species</span></li> </ul> </li> <li style="font-weight: 400;"><span style="font-weight: 400;">Second public release:</span> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">BLAST and potentially Ensembl VEP</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Increasing number of species</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Extended documentation</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Comparative data including homologues and alignments</span></li> </ul> </li> <li style="font-weight: 400;"><span style="font-weight: 400;">Final public release:</span> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Custom download</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Variation and regulation views</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Support for all species</span></li> </ul> </li> </ul> <h2><b>Ensembl-HAVANA manual gene annotation for human and mouse</b></h2> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Increasing depth of manual annotation based on long transcriptomic data (PacBio, ONT)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Introducing a refined version of Ensembl/GENCODE basic supported by transcriptomic, proteomic, conservation and functional data</span> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Support filtering of larger transcript set</span></li> </ul> </li> <li style="font-weight: 400;"><span style="font-weight: 400;">Refinement of protein-coding gene annotation and coordination with other reference databases to ensure improvements are reflected broadly:</span> <ul> <li style="font-weight: 400;"><span style="font-weight: 400;">Refseq (CCDS, MANE)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">UniProt (GIFTS)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">MGI – for mouse</span></li> </ul> </li> <li style="font-weight: 400;"><span style="font-weight: 400;">Introducing expert manual annotation of regulatory features, focussed on Enhancer-Promoter connections</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Complete review of all computational-only transcript models in Ensembl/GENCODE geneset</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Simplifying biotypes and capturing additional information about genes and transcripts in attributes</span></li> </ul> <h2><b>Improved infrastructure, applications and tools</b></h2> <ul><li>Improving robustness and consistency of the cross references pipeline, which adds associations between external resources and Ensembl identifiers </li><li><a rel="noreferrer noopener" href="https://trackhubregistry.org/" target="_blank">Track Hub Registry</a> re-implementation for improved maintainability </li><li>Extending functionality of Transcript Archive (<a href="http://dev-tark.ensembl.org/" target="_blank" rel="noreferrer noopener">Tark</a>)</li><li>Extending functionality of Genome Integration with FuncTion and Sequence  (<a rel="noreferrer noopener" href="https://www.ebi.ac.uk/gifts/" target="_blank">GIFTS</a>) – a common framework for UniProtKB/Ensembl mapping Public database of securely mapped sets of genes/proteins</li><li>A new REST API built to support our new Ensembl infrastructure</li><li>A new GraphQL service to provide an interface to Ensembl data and customisable API interaction</li><li>Upgrading Ensembl VEP to provide enhanced functionality for variant interpretation: improvements to core functionality and integration of relevant additional key datasets and further algorithms for the prediction of variant deleteriousness</li><li>FTP data explorer and support for GA4GH’s data retrieval service (DRS) to access these data</li></ul> </div> </article> </div> <footer class="site-info" itemscope itemtype="http://schema.org/WPFooter"> <a href="http://wordpress.org/" title="Semantic Personal Publishing Platform">Proudly powered by WordPress</a>. 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