Constructing knowledge graphs and their biomedical applications

Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing thes...

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Vydáno v:Computational and structural biotechnology journal Ročník 18; s. 1414 - 1428
Hlavní autoři: Nicholson, David N., Greene, Casey S.
Médium: Journal Article
Jazyk:angličtina
Vydáno: Netherlands Elsevier B.V 01.01.2020
Research Network of Computational and Structural Biotechnology
Elsevier
Témata:
automation
biotechnology
genomics
knowledge graphs
Lterature review
Machine learning
medicine
Natural language processing
Network embeddings
Review
Text mining
Text mining
Network embeddings
Natural language processing
Lterature review
knowledge graphs
Machine learning
ISSN:2001-0370, 2001-0370
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Shrnutí:Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing these processes. Biomedical knowledge graphs have often been constructed by integrating databases that were populated by experts via manual curation, but we are now seeing a more robust use of automated systems. A number of techniques are used to represent knowledge graphs, but often machine learning methods are used to construct a low-dimensional representation that can support many different applications. This representation is designed to preserve a knowledge graph’s local and/or global structure. Additional machine learning methods can be applied to this representation to make predictions within genomic, pharmaceutical, and clinical domains. We frame our discussion first around knowledge graph construction and then around unifying representational learning techniques and unifying applications. Advances in machine learning for biomedicine are creating new opportunities across many domains, and we note potential avenues for future work with knowledge graphs that appear particularly promising.
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ISSN:2001-0370
2001-0370
DOI:10.1016/j.csbj.2020.05.017