Ontology Alignment Evaluation Initiative

Large BioMed Track

Harmonisation of the OAEI 2011.5 outputs

We have harmonised the outputs of the systems participating in the OAEI 2011.5 FMA-NCI matching problem. Each system has been associated a weighted vote depending on its precision w.r.t. the UMLS reference alignment. Note that systems participating with two versions (e.g. GOMMA and LogMap) have been only considered once in the voting process.

The figure below summarises the evolution of the F-measure, Precision and Recall for the harmonised alignment set depending on the minimum required votes. For example the harmonised alignment set requiring 4.0 points of weighted votes has a precision of 0.971 and a recall of 0.369 w.r.t. the UMLS reference alignment. As expected precision increases and recall decreases as the required votes increase.

We have selected the harmonised alignment set with the highest F-measure (0.91) as reference alignment for the OAEI 2012 FMA-NCI matching problem. This set contains 2890 equivalence alignments that have been "at least" voted for two systems with weight 0.9. This reference alignment will be very useful to analyse how different a system is with respect to the others.

Note that this harmonised alignment have not been refined and it is known to lead to more than 14,000 unsatisfiable classes when integrated with FMA and NCI.