Harrow Ian, Jiménez-Ruiz Ernesto, Splendiani Andrea, Romacker Martin, Woollard Peter, Markel Scott, Alam-Faruque Yasmin, Koch Martin, Malone James, Waaler Arild
Pistoia Alliance Ontologies Mapping Project, Pistoia Alliance Inc, USA.
Department of Informatics, University of Oslo, Oslo, Norway.
J Biomed Semantics. 2017 Dec 2;8(1):55. doi: 10.1186/s13326-017-0162-9.
The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease.
Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results.
Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.
疾病与表型赛道旨在评估在源本体之间生成映射的本体匹配系统的相对性能。疾病和表型本体对于诸如数据挖掘、数据集成和知识管理等应用非常重要，以支持药物发现中的转化科学以及理解疾病遗传学。
（在21个参与OAEI的系统中）有11个系统能够应对疾病与表型赛道中的至少一项任务。与共识比对相比，AML、FCA-Map、LogMap(Bio)和PhenoMF系统在本体匹配方面取得了最佳结果。与人工编辑的映射相比，结果证明更具挑战性，这很可能是因为这些映射集主要包含包含关系而非等价关系。对唯一等价映射的人工评估表明，AML、LogMap(Bio)和PhenoMF系统具有最高的精确率结果。
四个系统在匹配疾病和表型本体方面表现出最高性能。这些系统在检测等价匹配方面表现良好，但在检测语义相似性方面存在困难。这在本体匹配系统的未来发展中值得更多关注。该评估结果表明，此类系统有助于在众多领域（如疾病和表型）中维护本体映射服务的策展人的工作流程中实现等价匹配自动化。
