SO
type: NamingSystem
node role: treeRoot
id:
  v: SO
text:
  status:
    v: generated
  div: Summary Defining URL http://terminology.hl7.org/NamingSystem/SO Version 1.0.0 Name SO Title Sequence Ontology Status active Definition "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." "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, Biosapiens DAS), or annotations encoded by GFF3." 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. 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." "The Sequence Ontology is part of OBO. It has close links to other ontology projects such as the RNAO consortium, and the Biosapiens polypeptide features." The content can be browsed here The content can be downloaded here For information on contributing, please see here To request a term or register feedback, see here Publisher Sequence Ontology Identifiers Type Value Preferred Period Comment URI http://www.sequenceontology.org true 2021-06-07 --> (ongoing) This is the URL as specified by the terminology owner, and is considered authoritative.
extension:
  url:
    v: http://hl7.org/fhir/5.0/StructureDefinition/extension-NamingSystem.url
  value:
    v: http://terminology.hl7.org/NamingSystem/SO
extension:
  url:
    v: http://hl7.org/fhir/5.0/StructureDefinition/extension-NamingSystem.version
  value:
    v: 1.0.0
extension:
  url:
    v: http://hl7.org/fhir/5.0/StructureDefinition/extension-NamingSystem.title
  value:
    v: Sequence Ontology
name:
  v: SO
status:
  v: active
kind:
  v: codesystem
date:
  v: 2023-12-11T00:00:00-00:00
publisher:
  v: Sequence Ontology
contact:
  name:
    v: Sequence Ontology; Karen Eilbeck (PI), Barry Moore (Software Developer), Shawn Rynearson (Software Developer)
  telecom:
    system:
      v: url
    value:
      v: http://www.sequenceontology.org
  telecom:
    system:
      v: email
  telecom:
    system:
      v: email
  telecom:
    system:
      v: email
description:
  v: "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." "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)." * 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." "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)." 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](ht…
unique id:
  type:
    v: uri
  value:
    v: http://www.sequenceontology.org
  preferred:
    v: true
  comment:
    v: This is the URL as specified by the terminology owner, and is considered authoritative.
  period:
    start:
      v: 2021-06-07