The Glycomics Ontology GlycO focuses on the glycoproteomics domain to model the structure and functions of glycans and glycoconjugates, the enzymes involved in their biosynthesis and modification, and the metabolic pathways in which they participate. GlycO is intended to provide both a schema and a sufficiently large knowledge base, which will allow classification of concepts commonly encountered in the field of glycobiology in order to facilitate automated reasoning and information analysis in this domain. A atom of the chemical element oxygen (atomic number 8). This canonical atom allows phosphates, which have several O atoms attached to a P atom, to be described. This canonical atom allows phosphates, which have several O atoms attached to a P atom, to be described. This canonical atom allows phosphates, which have several O atoms attached to a P atom, to be described. A linked_phosphate_residue contains only 3 oxygen atoms - the fourth O atom connected to the P atom belongs to the adjacent residue (e.g., a carbohydrate residue or another phosphate residue). An N-glycan_derived_oligoglycosyl_alditol that has antennae that originate with the addition of b-GlcpNAc residues to Man residues (e.g., by the action of GlcNAc transferases). A carbohydrate residue that is classified primarily by the positions of oxidized carbons in its structure. For example, a keto_sugar_residue has a carbonyl (oxidized) carbon (ketone) at a position other than C1. An aldo_residue has a carbonyl (aldehyde) at C1. An alditol residue has no oxidized carbons. Bisected N-glycans have a b-GlcpNAc residue that is attached to O4 of the core b-Manp residue (e.g., by GlcNAc-transferase III.) An atom in a specific chemical context within a nucleoside_base_residue A carbohydrate residue with an aldehyde at C1 The anomeric carbon of the reducing form of the sugar is a aldehyde aldo aldo CHEBI:24590 D-dRibf A 2-deoxy-D-ribofuranose residue alpha-D-galactose CHEBI:28061 a-D-Galp An alpha-D-galactopyranose residue a &945; D-Manp CHEBI:16024 A D-mannopyranose residue b-D-Xylp A beta-D-xylopyranose residue CHEBI:28161 &946; b A 6-deoxy-aldoHex_residue with galacto configuration Fuc galacto Fuc 1 1 A monoglycosyl moiety contains a single carbohydrate_residue. This moiety is glycosidically linked to another (presumably non-carboohydrate) moiety. An oxygen atom in a specific chemical context within a non-standard_residue A hydrolysis reaction that is catalyzed by an enzyme water A glycine residue Gly G A protein that catalyzes the transfer of a carbohydrate residue from a donor_substrate to an acceptor_substrate A beta-D-galactopyranose residue beta-D-galactose CHEBI:27667 b-D-Galp A D-galactose residue An organic carboxylic acid with an animo group on the alpha carbon. The building blocks of proteins are amino acids. In GlycO, instances of free amino acids are classified as amino_acid while amino acids that are part of a polypeptide are classified as amino_acid_residue. A molecule comprised predominantly of ribonucleotide_moieties, linked in a linear fashion by phosphodiester bonds. 5 A carbohydrate residue with 5 main-chain carbon atoms An isoleucine residue I Ile A atom of the chemical element phosphorous (atomic number 15). L-Araf An L-arabinofuranose residue N-acetyl-alpha-D-glucosamine a-D-GlcpNAc An N-acetyl-alpha-D-glucosamine residue with the anomeric configuration alpha A protein that is classified primarily by its biological or biochemical function. A carbohydrate residue with 6 main-chain carbon atoms, C1 as the anomeric carbon, and no oxygen atoms are missing 0 A molecule in whiich a significant protion is composed of lipid moieties (e.g. dolichol) Thr An L-trheonine residue T A molecule that is classified primarily by its capacity to act as the substrate of a glycosyl transferase that transfers a carbohydrate_residue or carbohydrate moiety from this molecule to another molecule. Although glycosyl transferases can catalyze bot the forward and backward reaction, the donor and acceptor are defined for the usual direction of the metabolic flux (i.e., biosynthesis of a glycan). 1 A carbohydrate residue that is classified primarily by the number of carbons in the main chain An L-aspartic acid residue Asp D A D-mannose residue a-D-GalpNAc An N-acetyl-alpha-D-galactosamine residue with the anomeric configuration alpha b-NeuAc A beta-N-acetyl-neuraminic acid residue An alpha-D-galactopyranosyl residue in the context of a monoglycosyl_moiety Having a five-membered ring, usually indicated by an italicized f. f o Not in a ring (as an alditol). THere is no shorthand nomenclature for this, but GLYDE uses "o" to specify an open chain form. Havig a six membered ring, indicated by an italicized p p A property that specifies the number of carbons in the ring that is part of a carbohydrate_residue's structure. A mannose residue Man manno A peptide containing only a few amino_acid_residues. 2 A free glycan is a carbohydrate that is not part of a glycocongugate. Examples are free oligosacharides and polysaccharides. 1 D A residue with the absolute configuration D An oligoglycosyl alditol derived from an N-glycan by enzymatic or chemical release from a glycoprotein/glycopeptide followed by reduction (e.g., with borohydride). The precursor of each of these oligoglycosyl alditols is an N-glycan_derived_oligosaccharide, whose precursor was an N-glycan. The residues of the N-glycan are the ultimate precursor residues for the residues in the oligoglycosyl alditol. An alpha-D-glucopyranosyl residue in the context of a monoglycosyl_moiety An L-arabinose residue L-Ara A carbohydrate residue with an aldehyde at C1 and six atoms in the ring (pyranose) a-L-Fucp An L-Fucp residue with the alpha anomeric configuration A nonreducing sugar residue with a 5-membered ring, usually represented by the italicized letter f. An N-glycan_derived_oligoglycosyl_alditol that has a b-D-GlcpNAc residue linked to O4 of the core b-D-Manp residue. A non-standard residue in a specific chemical context An N-glycan_derived_oligoglycosyl_alditol that has ONLY mannosyl residues attached to the core. A beta-D-ribofuranose residue An L-galactopyranose residue L-Galp A beta-L-fucopyranosyl residue in the context of a monoglycosyl_moiety 4 A carbohydrate residue with 4 main-chain carbon atoms A D-galactofuranose residue D-Galf A D-N-acetyl-galactosame residue with the pyranose ring form N-acetyl-D-galactosamine D-GalpNAc CHEBI:28037 A reducing N-acetyl-D-glucosame residue D-GlcNAc A peptide molecule that contains many amino_acid_residues. An L-proline residue P Pro An molecule consisting of a few carbohydrate_residues with a reducing-carbohydrate_residue at the reducing end A nitrogen atom in a specific chemical context within a non-standard_residue A beta-N-acetyl-alpha-D-galactosamine residue in the chemical context of an N-glycan N-acetyl-beta-D-galactosamine CHEBI:28497 b-D-GalpNAc gluco A carbohydrate residue that corresponds to a glucose in which O2 is replced by a nitrogen GlcN L-Galf An L-galactofuranose residue A glycosylated polypeptide (in which the peptide contains many amino_acid_residues). 1 An oligopeptide with an O-glycan attached to at least one serine, threonine, or hydroxyproline residue. A non-standard residue in the chemical context of an N-glycan A polysaccharide attached to a peptide. A carbohydrate residue with ketone at C2 and 6 carbons in the main chain CHEBI:28518 a-D-Xylp An alpha-D-xylopyranose residue A carbohydrate residue with ketone in the main chain An acidic amino acid residue 5-deoxy deoxy 3-deoxy deoxy An N-glycan_derived_oligosaccharide that has a b-D-GlcpNAc residue linked to O4 of the core b-D-Manp residue. A protein with a defined catalytic activity. 1 An oligopeptide with an N-glycan attached to N4 of at least one asparagine residue. A carbohydrate residue with 7 main-chain carbon atoms 7 A D-galactopyranose residue D-Galp D-galactose CHEBI:17118 A GlcN residue with the absolute configuration D D-GlcN An atom in a specific chemical context within a carbohydrate_residue A carbohydrate residue that is missing an oxygen, as it has been replaced by another atom, such as H or N L A residue with the absolute configuration L 1 A carbohydrate moiety is the carbohydrate portion of a molecule, defined by the restriction that it contains at least one sugar residue. To avoid recursion, sugar residues are not themselves defined as carbohydrate moieties, although the carbohydrate moiety can contain exactly one sugar residue. A ribose residue Rib ribo An oxygen atom in a specific chemical context within an amino_acid_residue CHEBI:17925 alpha-D-glucose An alpha-D-glucopyranose residue a-D-Glcp An alanine residue A Ala A 3-deoxy-D-manno-2-octulopyranosonic acid residue, commonly known as KDO D-KDOp D-dRib A 2-deoxy-D-ribose residue A beta-D-KDO residue b-D-KDOp A beta-D-2-deoxy-ribofuranosyl residue in the context of a nucleoside A molecular fragment that contains a ribose residue and a nucleoside_base residue. An alpha-N-glycolyl-neuraminic acid residue a-NeuGc A Fuc residue with absolute configuration L L-Fuc An atom or collection of atoms together form a chemical entity A molecular fragment that consists of a ribose residue, a nucleoside_base residue, and at least one linked_phosphate_residue. A (usually highly reactive) atomic or molecular entity that has unpaired electrons in a valence shell. b-L-Fucp An L-Fucp residue with the beta anomeric configuration N-acetyl N-acetyl 2-N-acetyl D-GalNAc A D-galactosame residue with an N-acetyl substituent GalNAc A beta-D-fructofuranose residue deoxy 2-deoxy A carbohydrate residue in which oxygen atom O2 is missing A hydrolysis reaction that is catalyzed by an enzyme and invloves the cleavage of a glycosidic bond. A carbohydrate residue in the chemical context of the glycan portion of an N-glycan. This includes all carbohydrate residues in N-glycans, their dol-P-P-linked precursors, and oligosaccharides released by cleavage of N-glycans The glycosidic oxygen - O1 - is part of the residue only when it is a reducing residue. For glycosyl residues, the glycosidic oxygen is formally specified as a component atom of the moiety to which the residue is covalently linked. For example, in the disaccharide maltose, O4 of the reducing glucose residue is also a glycosidic oxygen, and is not considered part of the (non-reducing) glucosyl residue that is linked to the reducing residue. A carbohydrate residue with an aldehyde at C1 that is not glycosidically linked to another moiety 0 An intramolecular_llink between two atoms A carbohydrate residue with 6 main-chain carbon atoms, C1 as the anomeric carbon, and oxygen atom O2 missing An alpha-L-galactofuranose residue a-L-Galf In hybrid N-glycans, the Mana1-6 arm contains only Man residues, while the Mana1-3 arm has antennae (each containing at least one b-GlcpNAc residue). . A glycoconjugate in which the non-carbohydrate moiety is primarily lipid A beta-D-xylopyranose residue in the chemical context of an N-glycan b-D-Xylp 0 0 0 0 0 0 0 The smallest piece of a chemical element, e.g., a carbon atom. 0 0 0 0 0 0 0 An molecule consisting of a few carbohydrate_residues with an alditol_residue at what would otherwise be the reducing end. A carbohydrate residue with an aldehyde at C1 and six main chain carbon atoms CHEBI:33917 A cysteine residue Cys C A carbon atom in a specific chemical context within an amino_acid_residue A glucosaminitol residue with the absolute configuration D D-glucosaminitol D-GlcN-ol An aromatic amino acid residue An alpha-D-mannopyranose residue in the chemical context of an N-glycan a-D-Manp An N-acetyl-alpha-D-glucosamine residue with the anomeric configuration beta b-D-GlcpNAc N-acetyl-beta-D-glucosamine CHEBI:28009 A chemical property of a residue that specifies its overall "handedness" . It s often designated as D or L for amino acids and sugars. Another class, the "sugar_configuration" specifies the configuration of all the assymetric centers for a carbohydrate_residue. A carbohydrate residue with ketone at C2, 6 carbons in the main chain, and no missing oxygen atoms D-Ribf A D-ribofuranose residue A galactose residue Gal CHEBI:18287 An a-L-Fucp residue in he context of an N-glycan a-L-Fucp b-D-dRibf A 2-deoxy-beta-D-ribofuranose residue An N-glycan_derived_oligoglycosyl_alditol in which the arm initiated with an alpha mannose attached to O6 of the core b-D-Manp residue contains only Man residues, while the the arm initiated with an alpha mannose attached to O3 of the core b-D-Manp residue has antennae (each containing at least one b-GlcpNAc residue). His H A histidine residue A sulfur-containing amino acid residue A biomolecule that has peptide moiety (amino acids connected by peptide bonds), plus a carbohydrate moiety. In GlycO, this class includes molecules with peptide moieties of different sizes, that is, it includes glycoproteins and glycopeptides. a-D-Manp An alpha-D-mannopyranose residue CHEBI:28729 An alpha-D-KDO residue a-D-KDOp S Ser A serine residue An alditol residue with 6 main chain carbons A molecular_property of an enzyme A molecule that is a biosynthetic precursor to N-linked glycans and contains a dolichol pyrophosphate aglycon. The N-glycan_core_a-D-GlcpNAc_A is linked to the pyrophosphate by an alpha-linkage. A biomolecule that is composed primarily of amino acids connected in a linear fashion by peptide bonds. In GlycO, oligopeptides (which contain only a few amino_acid_residues) and proteins (which contain many amino_acid_residues) are both classified as peptides. 1 a-D-Fruf An alpha-D-fructofuranose residue An alpha-D-N-acetyl-glucopyranosaminyl residue in the context of a monoglycosyl_moiety A molecue consisting of a single reducing_carbohydrate_residue. 1 A hydrogen atom in a specific chemical context within a nucleoside_base_residue H High-mannose N-glycans have ONLY mannosyl residues attached to the core. An alpha-N-glycolyl-neuraminic acid residue in the chemical context of an N-glycan a-NeuGc A carbohydrate residue with an aldehyde at C1 and five main chain carbon atoms An alpha-L-fucopyranosyl residue in the context of a monoglycosyl_moiety A beta-D-galactopyrano residue in the chemical context of an N-glycan CHEBI:27667 beta-D-galactose b-D-Galp A link between two molecular_fragments in the same molecule. The class intramolecular_link includes links between moieties (e.g., the link between a glycan_moiety and a peptidemoiety), between residues (e.g., between a mannose residue and a GlcNAc residue) and between atoms (e.g., between C1 of a mannose residue and O4 of a GlcNAc residue. Links are thus hierarchical, and a higher-order link embodies the lower-order links that specify more structural detail. A atom of the chemical element carbon (atomic number 6). a-NeuNAc An alpha-N-acetyl-neuraminic acid residue (pyranose) in the chemical context of an N-glycan a-Neup5Ac a-Neu5Ac CHEBI:17012 A atom of the chemical element hydrogen (atomic number 1). A molecular_property of a glycosyl transferase that specifies whether the reaction catalyzed by the enzyme results in the inversion of retention of the anomeric configuration of the carbohydrate_residue that is transferred. A molecule comprised