Table 5

Reasoner-inferred links for both human and mouse

HP (human)

MP (mouse)


Number of is_a relationships asserted in ontology

10,162

7,950

Number of is_a relationships that can be inferred automatically

1,421

2,922

Number of novel is_a relationships proposed (unvetted)

407

478


To validate our approach, we attempted to derive existing non-redundant relationships in two phenotype ontologies based on equivalence mappings and external ontologies. The first row is the number of relationships manually asserted by the ontology editors. The second row is the number of these asserted relationships that we can independently infer from first principles. The final row is the number of novel new relationships found by the reasoner - some of these will be false positives, but others will represent genuine missing links in the ontology. A higher proportion was yielded for mouse due to the higher number of mappings (Table 3; we only expect to recapitulate relationships when we have mappings).

Mungall et al. Genome Biology 2010 11:R2   doi:10.1186/gb-2010-11-1-r2

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