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 genomics life science obo ontology region ribonucleic acid rna sequence annotation sequence feature structure transcriptomics

Version

2024-11-18

License

CC-BY-4.0

Links

Homepage Repository OBO OWL

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

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

Pattern for RDF URIs

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

Example RDF URI

http://purl.obolibrary.org/obo/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 , 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.

Contact

Karen Eilbeck   0000-0002-0831-6427   keilbeck

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

Appears In (1)

PCL

In Collection (2)

FHIR External Terminologies Synapse.org external links

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 13 mappings to external registries with 3 unique external prefixes.

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. Some providers may use a different example, which is displayed in the table below. 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.