Proposed formal definition of a stage A part of the lifetime event of an entity –Lifetime event of a cell (e.g. cell cycle) –Lifetime event of an organism (e.g. developmental) development stage boundaries are typically fiat Stages are therefore occurrents –subdivisions of lifetime event on time axis –4D entities we could take a video of a stage –contrast with anatomical continuants e.g. cells, organisms, organs we could take a photo of a continuant –continuants participate in stages

Relationships between stages Substages can be part_of superstages –Segmentation:14_somites part_of Segmentation:14-19_somites Stages preceded_by other stages –2nd instar larval stage preceded_by 1st instar larval stage

Relationship between continuants and stages An organism (continuant) participates in its lifetime event (occurrent) throughout its entire existence Parts of the organism start and end during different stages –e.g. neural plate starts_during Segmentation:14-19_somites –note: not necessarily formation of a new entity - may be a single entity ‘e’ instantiating different types during different stages (transformation_of)

Accounting for variation We can’t always pin down the stage at which an anatomical entity type is first (or last) instantiated –natural variation between organisms –variation between subtypes Solution: new relations –starts_during_or_after –ends_during_or before

1414 … …44 presumptive spinal cord [] neural plate [] neural keel [] neural rod [] neural tube [] spinal cord [] Blastula:SphereAdult Gastrula:90%-epiboly Gastrula:Bud Segmentation Pharyngula:Prim somites somites somites transformation_of [ ] starts_during_or_after ends_during_or_before

Inferring process relationships presumptive spinal cord neural plate neural keel neural rod neural tube spinal cord transformation_of neural tube formation neural tube development neural plate formation neural plate development has_participant AO GO part_ofpreceded_by

Y [] X [] [ ] starts_during_or_after ends_during_or_before part_of X3 part_of Y3 X4 part_of Y4 X part_of Y during 3-4 or