Dealing with the Ambiguity of Glycan Substructure Search |
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| Authors: | Vincenzo Daponte Catherine Hayes Julien Mariethoz Frederique Lisacek |
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| Affiliation: | 1.Department of Computer Science, University of Geneva, 1227 Geneva, Switzerland; (C.H.); (J.M.);2.Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland;3.Section of Biology, University of Geneva, 1211 Geneva, Switzerland |
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| Abstract: | The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large-scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating these data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge base was validated with GlyConnect data and benchmarked with the Glycowork library. GlySTreeM is shown to be fast, consistent, reliable and more flexible than existing solutions for matching parts of or whole glycan structures. The model is also well suited for painless future expansion. |
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| Keywords: | glycan structure knowledge representation pattern recognition ontology semantic web |
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