Tackling the challenges of matching biomedical ontologies.
Tackling the challenges of matching biomedical ontologies.
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DOI：
10.1186/s13326-017-0170-9
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发表时间：
2018-01-15
影响因子：
1.9
通讯作者：
Cruz IF
中科院分区：
文献类型：
--
作者：
Faria D;Pesquita C;Mott I;Martins C;Couto FM;Cruz IF
由于生物医学领域的复杂性和本体本身的特点，生物医学本体对本体匹配提出了一些挑战。本体匹配评估计划（OAEI）中的生物医学轨道刺激了能够应对这些挑战的匹配系统的发展，并对其一般性能进行了基准测试。在这项研究中，我们剖析了匹配系统所采用的策略，以解决匹配生物医学本体的挑战，并衡量挑战本身对匹配性能的影响，使用的MatchementMakerLight（AML）系统作为本研究的平台。我们证明，大多数最先进的本体匹配系统实现的基于哈希的搜索策略的线性复杂性对于有效匹配大型生物医学本体至关重要。我们表明，占所有词汇注释（例如，标签和同义词）导致F-度量的实质性改进，并且考虑不同类型的注释的可靠性通常也导致显著的改进。最后，我们表明，交叉引用是一个可靠的信息来源，当使用生物医学本体作为背景知识，它通常是更可靠的，使用它们作为介质，而不是进行词汇扩展。我们预计，翻译传统的匹配算法的哈希为基础的搜索范式将是该领域的未来发展的一个重要方向。改进在OAEI生物医学轨道上进行的评价也很重要，因为如果没有适当的参考比对，就只能确定匹配系统或策略。然而，很明显，为了解决生物医学本体所带来的各种挑战，本体匹配系统必须能够有效地将联合收割机多种策略组合成一个成熟的匹配方法。本文的在线版本（doi：10.1186/s13326-017-0170-9）包含补充材料，可供授权用户使用。
Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Ontology Matching Evaluation Initiative (OAEI) have spurred the development of matching systems able to tackle these challenges, and benchmarked their general performance. In this study, we dissect the strategies employed by matching systems to tackle the challenges of matching biomedical ontologies and gauge the impact of the challenges themselves on matching performance, using the AgreementMakerLight (AML) system as the platform for this study. We demonstrate that the linear complexity of the hash-based searching strategy implemented by most state-of-the-art ontology matching systems is essential for matching large biomedical ontologies efficiently. We show that accounting for all lexical annotations (e.g., labels and synonyms) in biomedical ontologies leads to a substantial improvement in F-measure over using only the primary name, and that accounting for the reliability of different types of annotations generally also leads to a marked improvement. Finally, we show that cross-references are a reliable source of information and that, when using biomedical ontologies as background knowledge, it is generally more reliable to use them as mediators than to perform lexical expansion. We anticipate that translating traditional matching algorithms to the hash-based searching paradigm will be a critical direction for the future development of the field. Improving the evaluation carried out in the biomedical tracks of the OAEI will also be important, as without proper reference alignments there is only so much that can be ascertained about matching systems or strategies. Nevertheless, it is clear that, to tackle the various challenges posed by biomedical ontologies, ontology matching systems must be able to efficiently combine multiple strategies into a mature matching approach. The online version of this article (doi:10.1186/s13326-017-0170-9) contains supplementary material, which is available to authorized users.
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