Figure 1

Outline of an ontology of cell parts and its use to describe cell phenotypes. The figure shows a structure by which cell phenotypes, here for epithelial cells, mesenchymal cells and embryonic stem cells (ESC), can be formally represented, using entity terms (shown on the left hand side) and PATO-analogous quality modifiers (shown on the right hand side). Terms referring to cells are indicated in yellow, terms relating to structures in red, to ultrastructures in blue, and to molecules in green. With the exception of “is_a”, all relations are meant to have an all-some syntax, i.e. “Tight junction has_part Occludin” means: For all instances x of the type Tight junction there is some y that is an instance of the type Occludin such that x has part y.