The following ontologies were tested using jcel 0.12.0 and the CEL Plug-in 0.5.0 to compare execution times. Specifications:

• operating system : Linux, kernel 2.6.27
• memory : 4 GB
• processor 1 model name : Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz
• processor 1 cpu MHz : 1998.000
• processor 2 model name : Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz
• processor 2 cpu MHz : 1998.000

ontology	input	output	number of entries	jcel memory	jcel time	CEL time
Gene Ontology	owl	xml	154489	89 MB	2.8 s	3.2 s
NCI Thesaurus	owl	xml	346887	588 MB	6.2 s	10.2 s
CEL GALEN	owl	xml	6836237	301 MB	51 s	134 s
Not GALEN	owl	xml	224565	50 MB	2.7 s	5.2 s
Foundational Model of Anatomy			9576858	480 MB	149 s	2388 s
SNOMED CT			143039451	2378 MB	1109 s	705 s

The following ontologies were tested using jcel 0.8.0 and the CEL Plug-in 0.4.0 to compare execution times. Specifications:

• operating system : Linux, kernel 2.6.27
• memory : 4 GB
• processor 1 model name : Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz
• processor 1 cpu MHz : 1998.000
• processor 2 model name : Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz
• processor 2 cpu MHz : 1998.000

ontology	input	output	number of entries	jcel memory	jcel time	CEL time
Gene Ontology	krss owl	xml	142254	91 MB	3 s	9 s
CEL GALEN	krss owl	xml	23807869	422 MB	63 s	148 s
Not GALEN	krss owl	xml	445989	73 MB	3 s	6 s
Foundational Model of Anatomy			1290687	1329 MB	116 s	2315 s
SNOMED CT			522296612	2490 MB	2945 s	810 s