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Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling

Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
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Current address: EDP Patent Attorneys, 6708 WH Wageningen, The Netherlands.
Metabolites 2019, 9(2), 28; https://doi.org/10.3390/metabo9020028
Received: 28 December 2018 / Revised: 24 January 2019 / Accepted: 31 January 2019 / Published: 6 February 2019
Genome-scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used in different research areas, ranging from systems medicine to biotechnology. However, the different naming conventions (namespaces) of databases used to build GEMs limit model reusability and prevent the integration of existing models. This problem is known in the GEM community, but its extent has not been analyzed in depth. In this study, we investigate the name ambiguity and the multiplicity of non-systematic identifiers and we highlight the (in)consistency in their use in 11 biochemical databases of biochemical reactions and the problems that arise when mapping between different namespaces and databases. We found that such inconsistencies can be as high as 83.1%, thus emphasizing the need for strategies to deal with these issues. Currently, manual verification of the mappings appears to be the only solution to remove inconsistencies when combining models. Finally, we discuss several possible approaches to facilitate (future) unambiguous mapping. View Full-Text
Keywords: identifier multiplicity; name ambiguity; databases; naming conventions; standardization; chemical nomenclature; GEM; GEM interoperability identifier multiplicity; name ambiguity; databases; naming conventions; standardization; chemical nomenclature; GEM; GEM interoperability
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Pham, N.; van Heck, R.G.A.; van Dam, J.C.J.; Schaap, P.J.; Saccenti, E.; Suarez-Diez, M. Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. Metabolites 2019, 9, 28.

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