Class: cto:CL 0000113 SubClassOf:
hasNucleation some pato:PATO 0001407 Fig. 5. Mononuclear Phagocyte described in Manchester OWL syntax generated form the OPPL 2 pattern in figure 4 (PATO 0001407 is the identifier for *mononucleate*)

## 3 Use Case And Evaluation

In order to evaluate Populous in a real ontology building scenario, it has been used to populate a template for gathering knowledge about the kidney and urinary system. The kidney is a complex organ composed of several distinct anatomical compartments that together enable the filtration of waste from the blood in the form of urine. Each of the kidney compartments is formed from a wide variety of cell types, and the specificity of the compartments relies on these specialised cell functions. The Kidney and Urinary Pathway Ontology (KUPO) [12]
describes kidney cells, their function and their anatomical locations. KUPO is being built to annotate and integrate a variety of KUP related data held in the Kidney and Urinary Pathway Knowledge Base (KUPKB)9.

A simple template was designed for experts from the KUP domain to capture the relationships between cell types, their anatomical location and their biological functions. The template has three main columns; column A is for entering cell type terms, column C is for anatomy terms and column D for biological process terms. Populous was used to constrain the allowable values in columns A, C
and D to concepts from the Open Biomedical Ontology Cell Type Ontology [4],
subclasses or part of the Kidney or *Urinary system* concepts from the Mouse Adult Gross Anatomy Ontology [9], and all subclasses of the *Biological Process* concept from the Gene Ontology [20], respectively. The experts were instructed that the relationship between concepts in column A and C was *part of*, and the relationship between column A and D, *participates in*. For concepts that were related to multiple concepts they were allowed to list concepts in a cell separated by a comma. Figure 6 is a screen shot of Populous populated with data from the domain experts.

In order to transform the tabular data into an OWL representation the OPPL
pattern in Figure 7 was created by the ontology engineers. This pattern states that a cell type is equivalent to a cell that is *part* of an anatomy term and a subclass of cells that participate in biological processes.10 For both restrictions the existential (*some*) quantification is used. The two differentia in this pattern for a cell genus are the anatomical location and the biological process, which is retrieved from column A, B and C respectively in the template. The entire KUP ontology is generated from the template data combined with the ontology