The Sequence Ontology: Molecules project came about as an offshoot of SO for these reasons:
- Sequence features as defined by SO are generically dependent continuants: that is, the sequence features inhere within the bearer molecules (the independent continuants). Therefore SO itself does not represent molecules. See footnote.
- There is a gap among the other neighboring OBO ontologies (chEBI, RNAO, PRO) which excludes polymeric biological molecules. These are the kinds of molecules within which sequence features inhere.
- The development of SOM facilitates automatic ontology development by cross products between OBO ontologies.For example, will be of use to RNAO development by providing the types of polymeric molecules not currently present in existing ontologies such as ChEBI, with which to associate RNA annotations.
SOM is tied closely to SO and equivalent terms share the numerical part of their ID, for example intron as a feature and intron as an RNA molecule.
Evolution of the Sequence Ontology terms and relationships. J Biomed Inform. 2010 Mar 10. [Epub ahead of print] Mungall CJ, Batchelor C, Eilbeck K. This paper is available as a pre-print on the SO site.
footnote: for more discussion of dependent and independent continuants see BFO and OBO foundry papers.