| Title | Towards a knowledge graph for pre-/probiotics and microbiota-gut-brain axis diseases |
| Author | |
| Publication Years | 2022-11-08
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| DOI | |
| Source Title | |
| EISSN | 2045-2322
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| Volume | 12Issue:1 |
| Abstract | Scientific publications present biological relationships but are structured for human reading, making it difficult to use this resource for semantic integration and querying. Existing databases, on the other hand, are well structured for automated analysis, but do not contain comprehensive biological knowledge. We devised an approach for constructing comprehensive knowledge graphs from these two types of resources and applied it to investigate relationships between pre-/probiotics and microbiota-gut-brain axis diseases. To this end, we created (i) a knowledge base, dubbed ppstatement, containing manually curated detailed annotations, and (ii) a knowledge base, called ppconcept, containing automatically annotated concepts. The resulting Pre-/Probiotics Knowledge Graph (PPKG) combines these two knowledge bases with three other public databases (i.e. MeSH, UMLS and SNOMED CT). To validate the performance of PPKG and to demonstrate the added value of integrating two knowledge bases, we created four biological query cases. The query cases demonstrate that we can retrieve co-occurring concepts of interest, and also that combining the two knowledge bases leads to more comprehensive query results than utilizing them separately. The PPKG enables users to pose research queries such as "which pre-/probiotics combinations may benefit depression?", potentially leading to novel biological insights. |
| URL | [Source Record] |
| Indexed By | |
| Language | English
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| SUSTech Authorship | Others
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| WOS Accession No | WOS:000880437400002
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| Scopus EID | 2-s2.0-85141893932
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| Data Source | Scopus
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| Citation statistics |
Cited Times [WOS]:0
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| Document Type | Journal Article |
| Identifier | http://kc.sustech.edu.cn/handle/2SGJ60CL/411794 |
| Department | Department of Computer Science and Engineering |
| Affiliation | 1.Department of Computer Science,Center for Integrative Bioinformatics,Vrije Universiteit Amsterdam,Amsterdam,1081 HV,Netherlands 2.Knowledge Representation and Reasoning Group,Department of Computer Science,Vrije Universiteit Amsterdam,Amsterdam,1081 HV,Netherlands 3.Department of Computer Science and Engineering,Southern University of Science and Technology,Shenzhen,518055,China |
| Recommended Citation GB/T 7714 |
Liu，Ting,Lan，Gongjin,Feenstra，K. Anton,et al. Towards a knowledge graph for pre-/probiotics and microbiota-gut-brain axis diseases[J]. Scientific reports,2022,12(1).
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| APA |
Liu，Ting,Lan，Gongjin,Feenstra，K. Anton,Huang，Zhisheng,&Heringa，Jaap.(2022).Towards a knowledge graph for pre-/probiotics and microbiota-gut-brain axis diseases.Scientific reports,12(1).
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| MLA |
Liu，Ting,et al."Towards a knowledge graph for pre-/probiotics and microbiota-gut-brain axis diseases".Scientific reports 12.1(2022).
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