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

Pham, Nhung; Heck, Ruben G. A. van; Dam, Jesse C. J. van; Schaap, Peter J.; Saccenti, Edoardo; Suárez-Diez, María

doi:10.1101/503664

Cited by 2 publications

(1 citation statement)

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“…Metabolic models describe the inter-conversion of metabolites via biochemical reactions catalyzed by enzymes, providing snapshots of the metabolism under a given genetic or environmental condition [1,2]. Metabolic models of metabolism have proven to be an important tool in studying systems biology and have been successfully applied to various research fields, ranging from metabolic engineering to system medicine [3–7].…”

Section: Introductionmentioning

confidence: 99%

Hierarchical Harmonization of Atom-Resolved Metabolic Reactions Across Metabolic Databases

Huan

Moseley

2021

Preprint

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Metabolic models have been proven to be useful tools in system biology and have been suc-cessfully applied to various research fields in a wide range of organisms. A relatively complete metabolic network is a prerequisite for deriving reliable metabolic models. The first step in con-structing metabolic network is to harmonize compounds and reactions across different metabolic databases. However, effectively integrating data from various sources still remains a big chal-lenge. Incomplete and inconsistent atomistic details in compound representations across data-bases is a very important limiting factor. Here, we optimized a subgraph isomorphism detection algorithm to validate generic compound pairs. Moreover, we defined a set of harmonization re-lationship types between compounds to deal with inconsistent chemical details while successfully capturing atom-level characteristics, enabling a more complete enabling compound harmoniza-tion across metabolic databases. In total, 15,704 compound pairs across KEGG (Kyoto Encyclo-pedia of Genes and Genomes) and MetaCyc databases were detected. Furthermore, utilizing the classification of compound pairs and EC (Enzyme Commission) numbers of reactions, we estab-lished hierarchical relationships between metabolic reactions, enabling the harmonization of 3,856 reaction pairs. In addition, we created and used atom-specific identifiers to evaluate the con-sistency of atom mappings within and between harmonized reactions, detecting some con-sistency issues between the reaction and compound descriptions in these metabolic databases.

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Section: Introductionmentioning

confidence: 99%

Hierarchical Harmonization of Atom-Resolved Metabolic Reactions Across Metabolic Databases

Huan

Moseley

2021

Preprint

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A Systematic Assessment Of Current Genome-Scale Metabolic Reconstruction Tools

Mendoza

Olivier

Molenaar

et al. 2019

Preprint

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Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. However, these platforms, as yet, have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality, genome-scale metabolic models. It is therefore unclear for potential users which tool best fits the purpose of their research. In this work, we performed a systematic assessment of the current genome-scale reconstruction software platforms. To meet our goal, we first defined a list of features for assessing software quality related to genome-scale reconstruction, which we expect to be useful for the potential users of these tools. Subsequently, we used the feature list to evaluate the performance of each tool. In order to assess the similarity of the draft reconstructions to high-quality models, we compared each tool's output networks with that of the high-quality, manually curated, models of Lactobacillus plantarum and Bordetella pertussis, representatives of gram-positive and gram-negative bacteria, respectively. We showed that none of the tools outperforms the others in all the defined features and that model builders should carefully choose a tool (or combinations of tools) depending on the intended use of the metabolic model. Author SummaryMetabolic networks that comprise biochemical reactions at genome-scale have become very useful to study and predict the phenotype of important microorganisms. Several software platforms exist to build these metabolic networks. Based on different approaches and utilizing a variety of databases it is, unfortunately, unclear what are the best scenarios to use each of these tools. Hence, to understand the potential uses of these tools, we created a list of relevant features for metabolic reconstruction and we evaluated the tools in all these categories. Here, we show that none of the tools is better than the other in all the evaluated categories; instead, each tool is more suitable for particular purposes. Therefore, users should carefully select the tool(s) that best fit the purpose of their research. This is the first time these tools are systematically evaluated and this overview can be used as a guide for selecting the correct tool(s) for each case. Current state of genome-scale reconstruction toolsHere we provide a brief description of the current reconstruction tools (see also S1 Table).AutoKEGGRec (2018). AutoKEEGRec [13] is an easy-to-use automated tool that uses the KEGG databases to create draft genome-scale models for any microorganism in that database. It runs in MATLAB and is compatible with COBRA Toolbox v3 [14]. One of the advantages of this tool is that multiple queries (microorganisms) can be processed in one run making it appropriate for cases where several microorganisms need to be reconstructe...

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

Cited by 2 publications

References 48 publications

Hierarchical Harmonization of Atom-Resolved Metabolic Reactions Across Metabolic Databases

Hierarchical Harmonization of Atom-Resolved Metabolic Reactions Across Metabolic Databases

A Systematic Assessment Of Current Genome-Scale Metabolic Reconstruction Tools

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