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} </style> <link rel="icon" href="http://www.sequenceontology.org/wp-content/uploads/2015/03/so_icon.png" sizes="32x32" /> <link rel="icon" href="http://www.sequenceontology.org/wp-content/uploads/2015/03/so_icon.png" sizes="192x192" /> <link rel="apple-touch-icon-precomposed" href="http://www.sequenceontology.org/wp-content/uploads/2015/03/so_icon.png" /> <meta name="msapplication-TileImage" content="http://www.sequenceontology.org/wp-content/uploads/2015/03/so_icon.png" /> </head> <body class="home page-template-default page page-id-153 custom-background"> <header id="head"> <div class="head-fixed"> <div class="head-top"> <div class="container"> <div class="head-nav"> <! --- Shawn removed this -->  </div> <div class="head-socials"> <ul> </ul> </div> <div class="clear"></div> </div> </div> </div>  <div class="head-logo"> <div class="container"> <div class="logo"> <a href="http://www.sequenceontology.org"><img src="http://www.sequenceontology.org/wp-content/uploads/2016/03/SOLogo.jpg" class="logo" alt="logo"></a> </div> </div> </div> </header><div class="content"> <div class="container"> <div class="post_content"> <article id="post-153" class="post_box post-153 page type-page status-publish hentry"> <h1>Welcome To SO</h1> <h3 style="text-align: left;">Welcome to the Sequence Ontology</h3> <p>This is the home page of the Sequence Ontology (SO). SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the <a href="http://www.geneontology.org/">Gene Ontology Consortium</a>. Contributors to SO include the <a href="http://www.gmod.org/">GMOD</a> community, model organism database groups such as <a href="http://www.wormbase.org/">WormBase</a>, <a href="http://www.flybase.org/">FlyBase</a>, <a href="http://www.informatics.jax.org/">Mouse Genome Informatics</a> group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. SO is also part of the Open Biomedical Ontologies library. Our aim is to develop an ontology suitable for describing the features of biological sequences. For questions, please send mail to the <a href="https://www.lists.utah.edu/wws/info/song-devel">SO developers mailing list</a>. For new term suggestions, please use the <a href="https://github.com/The-Sequence-Ontology/SO-Ontologies/issues">Term Tracker</a>.</p> <hr /> <h3 style="text-align: justify;">Introduction</h3> <p style="text-align: justify;">The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Examples are <b>binding_site</b> and <b>exon</b>. Biomaterial features are those which are intended for use in an experiment such as <b>aptamer</b> and <b>PCR_product</b>. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as “polycistronic” and “maternally imprinted”.</p> <p style="text-align: justify;">The Sequence Ontologies are provided as a resource to the biological community. They have the following obvious uses:</p> <ul style="text-align: justify;"> <li>To provide for a structured controlled vocabulary for the description of primary annotations of nucleic acid sequence, e.g. the annotations shared by a DAS server (<a href="http://www.biodas.org/documents/das2/das2_protocol.html">BioDAS</a>, <a href="http://www.biosapiens.info/page.php?page=das_portal">Biosapiens DAS</a>), or annotations encoded by <a href="http://www.sequenceontology.org/gff3.shtml">GFF3</a>.</li> <li>To provide for a structured representation of these annotations within databases. Were genes within model organism databases to be annotated with these terms then it would be possible to query all these databases for, for example, all genes whose transcripts are edited, or trans-spliced, or are bound by a particular protein. One such genomic database is <a href="http://www.gmod.org/wiki/Chado">Chado.</a></li> <li>To provide a structured controlled vocabulary for the description of mutations at both the sequence and more gross level in the context of genomic databases.</li> </ul> <p style="text-align: justify;">The Sequence Ontology is part of <a href="http://www.obofoundry.org/">OBO</a>. It has close links to other ontology projects such as the <a href="http://roc.bgsu.edu/">RNAO consortium</a>, and the <a href="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BS">Biosapiens polypeptide features</a>.</p> <hr /> <p style="text-align: justify;"> </article> <div class="clear"></div> </div> <div class="sidebar"> <div id="nav_menu-10" class="widget_box widget_nav_menu"><div class="menu-so_menu-container"><ul id="menu-so_menu-1" class="menu"><li class="menu-item menu-item-type-custom menu-item-object-custom current-menu-item current_page_item menu-item-home menu-item-254"><a href="http://www.sequenceontology.org" aria-current="page">Home</a></li> <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-258"><a href="http://www.sequenceontology.org/browser/obob.cgi">Browser</a></li> <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-295"><a href="https://github.com/The-Sequence-Ontology/SO-Ontologies">Current SO Ontology Files</a></li> <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-255"><a href="https://github.com/The-Sequence-Ontology">Software</a></li> <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-256"><a href="https://github.com/The-Sequence-Ontology/SO-Ontologies/issues">Request A Term</a></li> <li class="menu-item menu-item-type-post_type menu-item-object-page menu-item-305"><a href="http://www.sequenceontology.org/?page_id=296">Sequence Ontology Publications</a></li> <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-219"><a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gvf.md">GVF</a></li> <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-308"><a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md">GFF3</a></li> <li class="menu-item menu-item-type-post_type menu-item-object-page menu-item-289"><a href="http://www.sequenceontology.org/?page_id=259">About</a></li> <li class="menu-item menu-item-type-custom menu-item-object-custom menu-item-257"><a href="https://github.com/The-Sequence-Ontology/SO-Ontologies/issues">Issues</a></li> </ul></div></div> <div id="recent-posts-6" class="widget_box widget_recent_entries"> <h3 class="side_title">News</h3> <ul> <li> <a href="http://www.sequenceontology.org/?p=351">Request for feedback</a> </li> <li> <a href="http://www.sequenceontology.org/?p=330">The Molecular Sequence Ontology</a> </li> <li> <a href="http://www.sequenceontology.org/?p=111">Changes to the structure of the SO regarding miRNA.</a> </li> <li> <a href="http://www.sequenceontology.org/?p=89">Welcome to the Sequence Ontology</a> </li> </ul> </div></div> <div class="clear"></div> </div> </div> <footer id="foot"> <div class="main-foot"> <div class="container"> <div class="foot-col"> </div> <div class="foot-col"> </div> <div class="foot-col"> </div> <div class="clear"></div> </div> </div> <div class="bottom-foot"> <div class="container"> <p class="credits">2024 Sequence Ontology</p> </div> </div> </footer> <script type='text/javascript' src='http://www.sequenceontology.org/wp-includes/js/imagesloaded.min.js?ver=3.2.0'></script> <script type='text/javascript' src='http://www.sequenceontology.org/wp-includes/js/wp-embed.min.js?ver=5.1.19'></script> </body> </html>