HL7 Terminology (THO)
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This page is part of the HL7 Terminology (v6.0.0: Release) based on FHIR (HL7® FHIR® Standard) v5.0.0. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

: Sequence Ontology - XML Representation

Active as of 2023-12-11

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<NamingSystem xmlns="http://hl7.org/fhir">
  <id value="SO"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: NamingSystem SO</b></p><a name="SO"> </a><a name="hcSO"> </a><a name="SO-en-US"> </a><h3>Summary</h3><table class="grid"><tr><td>Defining URL</td><td>http://terminology.hl7.org/NamingSystem/SO</td></tr><tr><td>Version</td><td>1.0.0</td></tr><tr><td>Name</td><td>SO</td></tr><tr><td>Title</td><td>Sequence Ontology</td></tr><tr><td>Status</td><td>active</td></tr><tr><td>Definition</td><td><div><p>&quot;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.&quot;</p>
<p>&quot;The Sequence Ontologies are provided as a resource to the biological community. They have the following obvious uses:</p>
<ul>
<li>
<p>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>.&quot;</p>
</li>
<li>
<p>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>.</p>
</li>
<li>
<p>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.&quot;</p>
</li>
</ul>
<p>&quot;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>.&quot;</p>
<p>The content can be browsed <a href="http://www.sequenceontology.org/browser/obob.cgi">here</a></p>
<p>The content can be downloaded <a href="https://github.com/The-Sequence-Ontology/SO-Ontologies">here</a></p>
<p>For information on contributing, please see <a href="https://github.com/The-Sequence-Ontology/SO-Ontologies#contributing">here</a></p>
<p>To request a term or register feedback, see <a href="https://github.com/The-Sequence-Ontology/SO-Ontologies/issues">here</a></p>
</div></td></tr><tr><td>Publisher</td><td>Sequence Ontology</td></tr></table><h3>Identifiers</h3><table class="grid"><tr><td><b>Type</b></td><td><b>Value</b></td><td><b>Preferred</b></td><td><b>Period</b></td><td><b>Comment</b></td></tr><tr><td>URI</td><td>http://www.sequenceontology.org</td><td>true</td><td>2021-06-07 --&gt; (ongoing)</td><td>This is the URL as specified by the terminology owner, and is considered authoritative.</td></tr></table></div>
  </text>
  <url value="http://terminology.hl7.org/NamingSystem/SO"/>
  <version value="1.0.0"/>
  <name value="SO"/>
  <title value="Sequence Ontology"/>
  <status value="active"/>
  <kind value="codesystem"/>
  <date value="2023-12-11T00:00:00-00:00"/>
  <publisher value="Sequence Ontology"/>
  <contact>
    <name
          value="Sequence Ontology; Karen Eilbeck (PI), Barry Moore (Software Developer), Shawn Rynearson (Software Developer)"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.sequenceontology.org"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="keilbeck@genetics.utah.edu"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="barry.moore@genetics.utah.edu"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="shawn.rynearson@gmail.com"/>
    </telecom>
  </contact>
  <description
               value="&quot;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.&quot;

&quot;The Sequence Ontologies are provided as a resource to the biological community. They have the following obvious uses:

* 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 ([BioDAS](http://www.biodas.org/documents/das2/das2_protocol.html), [Biosapiens DAS](http://www.biosapiens.info/page.php?page=das_portal)), or annotations encoded by [GFF3](http://www.sequenceontology.org/gff3.shtml).&quot;

* 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 [Chado](http://www.gmod.org/wiki/Chado).

* 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.&quot;

&quot;The Sequence Ontology is part of [OBO](http://www.obofoundry.org/). It has close links to other ontology projects such as the [RNAO consortium](http://roc.bgsu.edu/), and the [Biosapiens polypeptide features](http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BS).&quot;

The content can be browsed [here](http://www.sequenceontology.org/browser/obob.cgi)

The content can be downloaded [here](https://github.com/The-Sequence-Ontology/SO-Ontologies)

For information on contributing, please see [here](https://github.com/The-Sequence-Ontology/SO-Ontologies#contributing)

To request a term or register feedback, see [here](https://github.com/The-Sequence-Ontology/SO-Ontologies/issues)"/>
  <uniqueId>
    <type value="uri"/>
    <value value="http://www.sequenceontology.org"/>
    <preferred value="true"/>
    <comment
             value="This is the URL as specified by the terminology owner, and is considered authoritative."/>
    <period>
      <start value="2021-06-07"/>
    </period>
  </uniqueId>
</NamingSystem>