PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list

Abstract

Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been veri¯ed, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been veri¯ed. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identi¯ers of the § § § Corresponding author. ¶ ¶ ¶ First and second author contributed equally to the paper.Journal of Bioinformatics and Computational Biology Vol. 12, No. 6 (2014) enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.

A hitchhiker’s guide to DNA-based microbiome analysis

“…Accuracy : The terminology about microbiome is sound and corresponds to what has been previously discussed in the literature (Marchesi & Ravel, 2015). I found that the terminology used in the section microbial function is not always clear and does not simplify the presentation of the associated concepts (Karp, 2000) (Thomas, Mi & Lewis, 2007) (Kotera et al, 2014).…”

Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction

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Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments

“…EC sub-subclasses (upto the third digit of the EC numbers) were used as the reaction annotation by EC. PIERO is a collection of terminology annotating substrate–product relationships in enzymatic reactions ( Kotera et al , 2014 ).…”

“…Our results show that the proposed method outperforms previous descriptor-based methods or existing graph alignment-based methods in the enzymatic reaction-likeness prediction for isomer-enriched reactions. It is also useful for reaction annotation that assigns potential reaction characteristics such as EC (Enzyme Commission) numbers ( McDonald and Tipton, 2014 ) and PIERO (Enzymatic Reaction Ontology for Partial Information) terms ( Kotera et al , 2014 ) to substrate–product pairs. Finally, we conducted a comprehensive enzymatic reaction-likeness prediction for all possible uncharacterized compound pairs, suggesting potential metabolic pathways for newly predicted substrate–product pairs.…”