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

Version

2021-11-22

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 includes the namespaceEmbeddedInLUI as true. The actual part that gets prefixed before the local unique identifier regex, otherwise known as the banana, is SO:. Therefore, you might see local unique identifiers written out as 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.

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

Providers are various services that resolve CURIEs to URLs. The example CURIE so:0001157 is used to demonstrate the provides available for so. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.