Constraints for representing transforming entities in bio-ontologies

Abstract. Things change—develop, mature morph—but not everything in the same way. Representing this knowledge in ontologies faces issues on three fronts: what the category of the participating objects are, which type of relations they involve, and where constraints should be added. More precise distinctions can be made by using OntoClean’s properties and a novel status property that is generalised from formal temporal conceptual data modeling. Criteria are identified, formulated in 17 additional constraints, and assessed on applicability for representing transformations more accurately. This enables developers of (bio-)ontologies to represent and relate entities more precisely, such as monocyte & macrophage and healthy & unhealthy organs.