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The GlycO Ontology in Protégé

The GlycO Ontology in Protégé. 3 Top-Level Classes are Defined in GlycO. The GlycO Ontology in Protégé. Semantics Include Chemical Context. This Class Inherits from 2 Parents. The GlycO Ontology in Protégé.

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The GlycO Ontology in Protégé

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  1. The GlycO Ontology in Protégé 3 Top-Level Classes are Defined in GlycO

  2. The GlycO Ontology in Protégé Semantics Include Chemical Context This Class Inherits from 2 Parents

  3. The GlycO Ontology in Protégé The -D-Manp residues in N-glycans are found in 8 different chemical environments

  4. b-D-GlcpNAc -(1-6)+ b-D-GlcpNAc -(1-2)- b-D-GlcpNAc -(1-2)+ b-D-GlcpNAc -(1-4)- a-D-Manp -(1-6)+ b-D-Manp -(1-4)- b-D-GlcpNAc -(1-4)- b-D-GlcpNAc a-D-Manp -(1-3)+ GlycoTree – A Canonical Representation of N-Glycans We give a residue in this position the same name, regardless of the specificstructure it resides in Semantics! N. Takahashi and K. Kato, Trends in Glycosciences and Glycotechnology, 15: 235-251

  5. Glyco Population • The next slides show the different steps that were necessary to populate GlycO with glycan structures from multiple sources.

  6. Ontology population workflow

  7. [][Asn]{[(4+1)][b-D-GlcpNAc] {[(4+1)][b-D-GlcpNAc] {[(4+1)][b-D-Manp] {[(3+1)][a-D-Manp] {[(2+1)][b-D-GlcpNAc] {}[(4+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp] {[(2+1)][b-D-GlcpNAc]{}}}}}}

  8. <Glycan> <aglycon name="Asn"/> <residue link="4" anomeric_carbon="1" anomer="b" chirality="D" monosaccharide="GlcNAc"> <residue link="4" anomeric_carbon="1" anomer="b" chirality="D" monosaccharide="GlcNAc"> <residue link="4" anomeric_carbon="1" anomer="b" chirality="D" monosaccharide="Man" > <residue link="3" anomeric_carbon="1" anomer="a" chirality="D" monosaccharide="Man" > <residue link="2" anomeric_carbon="1" anomer="b" chirality="D" monosaccharide="GlcNAc" > </residue> <residue link="4" anomeric_carbon="1" anomer="b" chirality="D" monosaccharide="GlcNAc" > </residue> </residue> <residue link="6" anomeric_carbon="1" anomer="a" chirality="D" monosaccharide="Man" > <residue link="2" anomeric_carbon="1" anomer="b" chirality="D" monosaccharide="GlcNAc"> </residue> </residue> </residue> </residue> </residue> </Glycan>

  9. EnzyO • The enzyme ontology EnzyO is highly intertwined with GlycO. While it’s structure is mostly that of a taxonomy, it is highly restricted at the class level and hence allows for comfortable classification of enzyme instances from multiple organisms.

  10. Putting it together • GlycO together with EnzyO contain all the information that is needed for the description of Metabolic pathways • e.g. N-Glycan Biosynthesis

  11. N-glycan_beta_GlcNAc_9 N-glycan_alpha_man_4 GNT-Vattaches GlcNAc at position 6 N-acetyl-glucosaminyl_transferase_V UDP-N-acetyl-D-glucosamine + alpha-D-Mannosyl-1,3-(R1)-beta-D-mannosyl-R2 <=> UDP + N-Acetyl-$beta-D-glucosaminyl-1,2-alpha-D-mannosyl-1,3-(R1)-beta-D-mannosyl-$R2 UDP-N-acetyl-D-glucosamine + G00020 <=> UDP + G00021 N-Glycosylation metabolic pathway GNT-Iattaches GlcNAc at position 2

  12. Pathway representation in GlycO Pathways do not need to be explicitly defined in GlycO. The residue-, glycan-, enzyme- and reaction descriptions contain all the knowledge necessary to infer pathways.

  13. Reaction R05987 catalyzed by enzyme 2.4.1.145 adds_glycosyl_residue N-glycan_b-D-GlcpNAc_13 Zooming in a little … The N-Glycan with KEGG ID 00015 is the substrate to the reaction R05987, which is catalyzed by an enzyme of the class EC 2.4.1.145. The product of this reaction is the Glycan with KEGG ID 00020.

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