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

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 , 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 Semantic Farm 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 Semantic Farm schema can be found here.

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

PCL

In Collection

FHIR External Terminologies Synapse.org external links

The metaregistry provides mappings between the Semantic Farm and other registries. There are 13 mappings to external registries for this resource with 3 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. 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 Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.