Improving ontologies by automatic reasoning and evaluation of logical definitions

BMC Bioinformatics

Table 1 10 External ontologies used for the MPO test-run

*Ontology*	*Number classes in Ontology*	*Fraction of terms referenced in logical definitions*
Chemical Entities of Biological Interest	44,843	2.71 %
Gene Ontology	35,090	4.35 %
Protein Ontology	26,727	0.18 %
Molecule Role Ontology	9,530	0.66 %
Uber-Anatomy (UBERON)	8,111	17.70 %
BRENDA Tissue Ontology	4,975	0.28 %
Adult Mouse Anatomical Dictionary	2,994	43.05 %
Phenotype, Attribute and Trait Ontology	2,283	23.87 %
Cell Ontology	1,510	30.20 %
Mouse Pathology	643	18.97 %
Total	140,453	7.45 %

Less than 10 % of the terms of the external ontologies are used by the logical definitions of the MPO terms. "Fraction of terms referenced in logical definitions" denotes the percentage of terms in the ontology that are members of the induced ancestral graph and are used by the logical definitions of the MPO terms.

ISSN: 1471-2105