GlycoEnzOnto: A GlycoEnzyme pathway and molecular function ontology

Theodore Groth; Alexander D. Diehl; Rudiyanto Gunawan; Sriram Neelamegham

doi:10.1093/bioinformatics/btac704

GlycoEnzOnto: A GlycoEnzyme pathway and molecular function ontology

SUNY Buffalo

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Abstract

Motivation: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan biosynthesis pathways. Results: We present GlycoEnzOnto, an ontology describing 403 human glycoEnzymes curated along 139 glycosylation pathways, 134 molecular functions and 22 cellular compartments. The pathways described regulate nucleotide-sugar metabolism, glycosyl-substrate/donor transport, glycan biosynthesis and degradation. The role of each enzyme in the glycosylation initiation, elongation/branching and capping/termination phases is described. IUPAC linear strings present systematic human/machine-readable descriptions of individual reaction steps and enable automated knowledge-based curation of biochemical networks. All GlycoEnzOnto knowledge is integrated with the Gene Ontology biological processes. GlycoEnzOnto enables improved transcript overrepresentation analyses and glycosylation pathway identification compared to other available schema, e.g. KEGG and Reactome. Overall, GlycoEnzOnto represents a holistic glycoinformatics resource for systems-level analyses.

Original language	English
Pages (from-to)	5413-5420
Number of pages	8
Journal	Bioinformatics
Volume	38
Issue number	24
DOIs	https://doi.org/10.1093/bioinformatics/btac704
State	Published - Dec 15 2022

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title = "GlycoEnzOnto: A GlycoEnzyme pathway and molecular function ontology",

abstract = "Motivation: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan biosynthesis pathways. Results: We present GlycoEnzOnto, an ontology describing 403 human glycoEnzymes curated along 139 glycosylation pathways, 134 molecular functions and 22 cellular compartments. The pathways described regulate nucleotide-sugar metabolism, glycosyl-substrate/donor transport, glycan biosynthesis and degradation. The role of each enzyme in the glycosylation initiation, elongation/branching and capping/termination phases is described. IUPAC linear strings present systematic human/machine-readable descriptions of individual reaction steps and enable automated knowledge-based curation of biochemical networks. All GlycoEnzOnto knowledge is integrated with the Gene Ontology biological processes. GlycoEnzOnto enables improved transcript overrepresentation analyses and glycosylation pathway identification compared to other available schema, e.g. KEGG and Reactome. Overall, GlycoEnzOnto represents a holistic glycoinformatics resource for systems-level analyses.",

author = "Theodore Groth and Diehl, \{Alexander D.\} and Rudiyanto Gunawan and Sriram Neelamegham",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s). Published by Oxford University Press.",

year = "2022",

month = dec,

day = "15",

doi = "10.1093/bioinformatics/btac704",

language = "English",

volume = "38",

pages = "5413--5420",

journal = "Bioinformatics",

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T1 - GlycoEnzOnto

T2 - A GlycoEnzyme pathway and molecular function ontology

AU - Groth, Theodore

AU - Diehl, Alexander D.

AU - Gunawan, Rudiyanto

AU - Neelamegham, Sriram

PY - 2022/12/15

Y1 - 2022/12/15

N2 - Motivation: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan biosynthesis pathways. Results: We present GlycoEnzOnto, an ontology describing 403 human glycoEnzymes curated along 139 glycosylation pathways, 134 molecular functions and 22 cellular compartments. The pathways described regulate nucleotide-sugar metabolism, glycosyl-substrate/donor transport, glycan biosynthesis and degradation. The role of each enzyme in the glycosylation initiation, elongation/branching and capping/termination phases is described. IUPAC linear strings present systematic human/machine-readable descriptions of individual reaction steps and enable automated knowledge-based curation of biochemical networks. All GlycoEnzOnto knowledge is integrated with the Gene Ontology biological processes. GlycoEnzOnto enables improved transcript overrepresentation analyses and glycosylation pathway identification compared to other available schema, e.g. KEGG and Reactome. Overall, GlycoEnzOnto represents a holistic glycoinformatics resource for systems-level analyses.

AB - Motivation: The 'glycoEnzymes' include a set of proteins having related enzymatic, metabolic, transport, structural and cofactor functions. Currently, there is no established ontology to describe glycoEnzyme properties and to relate them to glycan biosynthesis pathways. Results: We present GlycoEnzOnto, an ontology describing 403 human glycoEnzymes curated along 139 glycosylation pathways, 134 molecular functions and 22 cellular compartments. The pathways described regulate nucleotide-sugar metabolism, glycosyl-substrate/donor transport, glycan biosynthesis and degradation. The role of each enzyme in the glycosylation initiation, elongation/branching and capping/termination phases is described. IUPAC linear strings present systematic human/machine-readable descriptions of individual reaction steps and enable automated knowledge-based curation of biochemical networks. All GlycoEnzOnto knowledge is integrated with the Gene Ontology biological processes. GlycoEnzOnto enables improved transcript overrepresentation analyses and glycosylation pathway identification compared to other available schema, e.g. KEGG and Reactome. Overall, GlycoEnzOnto represents a holistic glycoinformatics resource for systems-level analyses.

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DO - 10.1093/bioinformatics/btac704

M3 - Article

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SN - 1367-4803

VL - 38

SP - 5413

EP - 5420

JO - Bioinformatics

JF - Bioinformatics

IS - 24

ER -

GlycoEnzOnto: A GlycoEnzyme pathway and molecular function ontology

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