Welcome to the Sequence Ontology
This is the home page of the Sequence Ontology Project (SO), a joint effort by genome annotation centres, and other groups using sequence annotation data, including: WormBase, FlyBase, the Mouse Genome Informatics group, and the Sanger Institute. We are a part of the Gene Ontology Project and the Open Biomedical Ontologies (OBO) . Our aim is to develop an ontology suitable for describing biological sequences. For questions, please send mail to the SO developers mailing list
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:
- To provide for a structured controlled vocabulary for the description of primary annotations of nucleic acid sequence, e.g. the annotations shared by a DAS server (BioDAS, Biosapiens DAS), or annotations encoded by GFF3.
- To provide for a structured representation of these annotations within databases. Were genes within model organism databases to be annotated with these terms then it would be possible to query all these databases for, for example, all genes whose transcripts are edited, or trans-spliced, or are bound by a particular protein. One such genomic database is Chado.
- To provide a structured controlled vocabulary for the description of mutations at both the sequence and more gross level in the context of genomic databases.
Current SO Ontology files
|Ontology||Latest CVS Revision||Current and Archived Releases||Description|
|SO with Composite Terms||so-xp.obo||so-xp.obo||Composite Terms Summary|
The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. OWL is generated from the obo file using go-perl. The resolvable URI for the current version of SO is http://purl.org/obo/owl/SO. As of Jan 25 2007, the transform has been updated from the old lossy transform to the new non-lossy mapping.