OAEI 2013::Large BioMed Track

Results OAEI 2013::Large BioMed Track

Results of the SNOMED-NCI matching problem

The following tables summarize the results for the tasks in the SNOMED-NCI matching problem.

LogMap-BK and ServOMap provided the best results in terms of both Recall and F-measure in Task 5 and Task 6, respectively. YAM++ provided the best results in terms of precision in Task 5 while AML-R in Task 6.

As in the previous matching problems, efficiency decreases as the ontology size increases. For example, in Task 6, only ServOMap and YAM++ could reach an F-measure higher than 0.7. Furthermore, the results were less positive than in the FMA-SNOMED matching problem, and thus, matching NCI against SNOMED represented another leap in complexity.

Task 5: SNOMED-NCI small fragments

**Table 1:** Results for the largebio task 5.
System	Time (s)	# Mappings	Scores			Incoherence Analysis
System	Time (s)	# Mappings	Precision	Recall	F-measure	Unsat.	Degree
LogMap-BK	444	13,985	0.894	0.677	0.770	≥40	≥0.05%
LogMap	433	13,870	0.896	0.672	0.768	≥47	≥0.06%
ServOMap	1,699	12,716	0.933	0.642	0.761	≥59,944	≥79.8%
AML-BK-R	397	13,006	0.920	0.648	0.760	≥32	≥0.04%
AML-BK	380	13,610	0.894	0.658	0.758	≥66,389	≥88.4%
AML-R	328	12,622	0.924	0.631	0.750	≥36	≥0.05%
YAM++	391	11,672	0.967	0.611	0.749	≥0	≥0.0%
AML	291	13,248	0.895	0.642	0.747	≥63,305	≥84.3%
Average	602	12,003	0.925	0.599	0.723	32,222	42.9%
LogMapLt	55	10,962	0.944	0.560	0.703	≥60,427	≥80.5%
GOMMA₂₀₁₂	221	10,555	0.940	0.537	0.683	≥50,189	≥66.8%
SPHeRe	2,486	9,389	0.924	0.469	0.623	≥46,256	≥61.6%
IAMA	99	8,406	0.965	0.439	0.604	≥40,002	≥53.3%

Task 6: NCI whole ontology with SNOMED large fragment

**Table 2:** Results for the largebio task 6.
System	Time (s)	# Mappings	Scores			Incoherence Analysis
System	Time (s)	# Mappings	Precision	Recall	F-measure	Unsat.	Degree
ServOMap	6,320	14,312	0.822	0.637	0.718	≥153,259	≥81.0%
YAM++	713	12,600	0.881	0.601	0.714	≥116	≥0.06%
AML-BK	571	11,354	0.918	0.564	0.699	≥121,525	≥64.2%
AML-BK-R	636	11,033	0.929	0.555	0.695	≥41	≥0.02%
LogMap-BK	1,088	12,217	0.871	0.576	0.693	≥1	≥0.001%
LogMap	1,233	11,938	0.882	0.570	0.692	≥1	≥0.001%
AML	570	10,940	0.927	0.549	0.689	≥121,171	≥64.1%
AML-R	640	10,622	0.938	0.539	0.685	≥51	≥0.03%
Average	1,951	11,581	0.880	0.549	0.674	72,365	38.3%
LogMapLt	132	12,907	0.802	0.560	0.660	≥150,773	≥79.7%
GOMMA₂₀₁₂	728	12,440	0.787	0.530	0.634	≥127,846	≥67.6%
SPHeRe	10,584	9,776	0.881	0.466	0.610	≥105,418	≥55.7%
IAMA	207	8,843	0.917	0.439	0.593	≥88,185	≥46.6%