The Molecular Sequence Ontology

The Molecular Sequence Ontology (MSO), a collaborative effort between Michael Sinclair (Postdoc in Eilbeck Lab), Mike Bada, and Karen Eilbeck, is nearing completion. The MSO is a companion to the Sequence Ontology for those who need to represent familiar SO entities as molecules rather than genome annotations. This occurs when, for example, SO entities must participate in physical or chemical processes defined by neighboring ontologies, or when catalytic activity is ascribed to the entity. In such cases the corresponding MSO entity should be used instead. In terms of the Basic Formal Ontology, SO entities are generically dependent continuants, and MSO entities are independent continuants. Henceforth, each SO entity will be defined as generically depending on its MSO counterpart, thus: SO:mRNA generically_depends_on MSO:mRNA.  One important consequence of this that will directly impact most users is that the upper-level taxonomy will change quite markedly.  The SO will no longer be composed of four sub-ontologies (i.e. sequence_feature, sequence_variant, sequence_collection, sequence_attribute) and will instead be kept as parallel as possible to the MSO’s taxonomy through all future development (for technical details, please consult our paper presented at the Bio-ontologies COSI of the ISMB 2018 conference).  There will be one encompassing top node, “biological sequence entity”, under which there is a set of subclasses organized according to a different scheme than the familiar SO.  Users may download the current, fully reasoned, working version of the MSO as an OWL file and examine the new hierarchy for themselves, beginning under “independent continuant”.  We will provide a news update once the MSO and the new SO have been officially released.