The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.

Prefix

so

Preferred Prefix

SO

Keywords

bioinformatics biology deoxyribonucleic acid dna gene genome life science obo ontology ribonucleic acid rna sequence sequence annotation sequence feature structure

Version

2024-06-05

License

CC-BY-4.0

Links

Homepage Repository OBO OWL

Contact

Karen Eilbeck   0000-0002-0831-6427   keilbeck

Pattern for Local Unique Identifiers

Local identifiers in Sequence types and features ontology should match this regular expression:
^\d{7}$

Example Local Unique Identifier

0001157   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Sequence types and features ontology should match this regular expression:
^SO:\d{7}$

Example CURIE

SO:0001157

MIRIAM Namespace Embedded in LUI

The legacy MIRIAM standard for generating CURIEs with this resource annotates the namespaceEmbeddedInLUI as true. This means that you may see local unique identifiers that include a redundant prefix and delimiter (also known as a banana) and therefore look like a CURIE. For Sequence types and features ontology, the banana looks like SO:. Therefore, you may see local unique identifiers for this resource that look like SO:0001157 (instead of the canonical form 0001157) and CURIEs for this resource that look like SO:SO:0001157 (instead of the canonical form SO:0001157). The Bioregistry will automatically strip off the banana when standardizing local unique identifiers and CURIEs.

Publications

• 2010 A standard variation file format for human genome sequences
• 2010 Evolution of the Sequence Ontology terms and relationships
• 2005 The Sequence Ontology: a tool for the unification of genome annotations

A summary of the relations in the Bioregistry schema can be found here.

Appears In (1) (bioregistry.schema:0000018 )

PCL

In Collection

FHIR External Terminologies

The metaregistry provides mappings between the Bioregistry and other registries. There are 12 mappings to external registries for this resource with 2 unique external prefixes.

When using this resource in RDF, the following URI format should be used:

http://purl.obolibrary.org/obo/SO_$1

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier 0001157 is used to demonstrate the providers available for Sequence types and features ontology. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.