Matching biomedical ontologies based on formal concept analysis

doi:10.1186/s13326-018-0178-9

CSpace > 数学所

	Matching biomedical ontologies based on formal concept analysis
	Zhao, Mengyi 1,2; Zhang, Songmao1 ; Li, Weizhuo 1,2; Chen, Guowei 1,2
	2018-03-19
发表期刊	JOURNAL OF BIOMEDICAL SEMANTICS
ISSN	2041-1480
卷号	9 页码:27
摘要	Background: The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. Methods: We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Results: Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign demonstrates the effectiveness of FCA-Map and its competitiveness with the top-ranked systems. FCA-Map can achieve a better balance between precision and recall for large-scale domain ontologies through constructing multiple FCA structures, whereas it performs unsatisfactorily for smaller-sized ontologies with less lexical and semantic expressions. Conclusions: Compared with other FCA-based OM systems, the study in this paper is more comprehensive as an attempt to push the envelope of the Formal Concept Analysis formalism in ontology matching tasks. Five types of formal contexts are constructed incrementally, and their derived concept lattices are used to cluster the commonalities among classes at lexical and structural level, respectively. Experiments on large, real-world domain ontologies show promising results and reveal the power of FCA.
关键词	Ontology matching Formal concept analysis Concept lattice
DOI	10.1186/s13326-018-0178-9
语种	英语
资助项目	National Key Research and Development Program of China[2016YFB1000902] ; Natural Science Foundation of China[61232015] ; Natural Science Foundation of China[61621003] ; Knowledge Innovation Program of the Chinese Academy of Sciences (CAS) ; Institute of Computing Technology of CAS
WOS研究方向	Mathematical & Computational Biology
WOS类目	Mathematical & Computational Biology
WOS记录号	WOS:000427962400001
出版者	BIOMED CENTRAL LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/405
专题	数学所
通讯作者	Zhang, Songmao
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, MADIS, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Zhao, Mengyi,Zhang, Songmao,Li, Weizhuo,et al. Matching biomedical ontologies based on formal concept analysis[J]. JOURNAL OF BIOMEDICAL SEMANTICS,2018,9:27.
APA	Zhao, Mengyi,Zhang, Songmao,Li, Weizhuo,&Chen, Guowei.(2018).Matching biomedical ontologies based on formal concept analysis.JOURNAL OF BIOMEDICAL SEMANTICS,9,27.
MLA	Zhao, Mengyi,et al."Matching biomedical ontologies based on formal concept analysis".JOURNAL OF BIOMEDICAL SEMANTICS 9(2018):27.