Developing a semantically rich ontology for the biobank-administration domain

Table 1 DL Queries executed on the Competency Test OWL file and results

Competency question	DL Query	Recall	Precision	Ratio	Reasoning time (in ms)
Which biobanks hold frozen specimens?	biobank and has_part some 'frozen specimen'	100%	100%	6/6	76.9
Which biobanks hold blood, plasma and serum?	biobank and has_part some 'blood plasma specimen' and has_part some 'blood serum specimen' and has_part some 'blood specimen'	100%	100%	5/5	53.2
Which blood plasma specimens are owned by one specific biobank organization?	'blood plasma specimen' and part_of some (biobank and 'is owned by' some {'Unseen University'})	100%	100%	6/6	45.4
Which departments of a specific university have members that are serving as biobank contacts?	department and 'has organization member' some (bearer_of some 'biobank contact role')	100%	100%	6/6	30.2
What are the e-mail addresses of all biobank contact persons at one specific biobank organization?	'email address' and 'is contact information about' some (bearer_of some 'biobank contact role' and 'is member of organization' some {'Unseen University'})	100%	100%	6/6	55.2

Each query is encoded in a separate test method in Scala using the Java OWL-API. Each method reloads the ontology, builds the necessary axiom from API calls, adds the axiom, executes the query, and removes the axiom from the ontology. Each trial was conducted by running each method 100 times and reporting the average running time in milliseconds. Ten trials were conducted.

ISSN: 2041-1480