A structured controlled vocabulary for sequence annotation, for the exchange of annotation data and for the description of sequence objects in databases.
SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. SO is also part of the Open Biomedical Ontologies library. Our aim is to develop an ontology suitable for describing the features of biological sequences. For questions, please send mail to the SO developers mailing list. For new term suggestions, please use the Term Tracker.
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. Examples are binding_site and exon. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as “polycistronic” and “maternally imprinted”.
The Sequence Ontologies are provided as a resource to the biological community. They have the following obvious uses:
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.
|so.owl||Main SO OWL release|
|so.obo||Main SO release in OBO Format|
|so/subsets/SOFA.owl||Sequence Ontology Feature Annotation (SOFA) subset (OWL)||This subset includes only locatable sequence features and is designed for use in such outputs as GFF3|
|so/subsets/SOFA.obo||Sequence Ontology Feature Annotation (SOFA) subset (OBO Format)||This subset includes only locatable sequence features and is designed for use in such outputs as GFF3|