The GlycO Ontology in Protégé
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Transcript of The GlycO Ontology in Protégé
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The GlycO Ontology in Protégé
3 Top-Level Classes are Defined in GlycO
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The GlycO Ontology in Protégé
Semantics Include Chemical Context
This Class Inherits from 2 Parents
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The GlycO Ontology in Protégé
The -D-Manp residues in N-glycans are found in 8 different chemical environments
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GlycoTree – A Canonical Representation of N-Glycans
N. Takahashi and K. Kato, Trends in Glycosciences and Glycotechnology, 15: 235-251
-D-GlcpNAc-D-GlcpNAc-D-Manp-(1-4)- -(1-4)-
-D-Manp -(1-6)+-D-GlcpNAc-(1-2)-
-D-Manp -(1-3)+-D-GlcpNAc-(1-4)-
-D-GlcpNAc-(1-2)+
-D-GlcpNAc-(1-6)+
We give a residue in this position the same name, regardless of the specific
structure it resides in
Semantics!
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• The next slides show the different steps that were necessary to populate GlycO with glycan structures from multiple sources.
Glyco Population
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Has CarbBank
ID?
IUPAC to LINUCS
LINUCS to GLYDE
Compare to Knowledge
Base
Already in KB?
YES
NO
Semagix Freedom knowledge extractor
Instance Data
YES: next Instance
Insert into KB
NO
Ontology population workflow
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Has CarbBank
ID?
IUPAC to LINUCS
LINUCS to GLYDE
Compare to Knowledge
Base
Already in KB?
YES
NO
Semagix Freedom knowledge extractor
Instance Data
YES: next Instance
Insert into KB
NO
[][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]{}}}}}}
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Has CarbBank
ID?
IUPAC to LINUCS
LINUCS to GLYDE
Compare to Knowledge
Base
Already in KB?
YES
NO
Semagix Freedom knowledge extractor
Instance Data
YES: next Instance
Insert into KB
NO
<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>
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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.
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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
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N-Glycosylation metabolic pathway
GNT-Iattaches GlcNAc at position 2
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
GNT-Vattaches GlcNAc at position 6
UDP-N-acetyl-D-glucosamine + G00020 <=> UDP + G00021
N-acetyl-glucosaminyl_transferase_VN-glycan_beta_GlcNAc_9N-glycan_alpha_man_4
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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.
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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.
Reaction R05987catalyzed by enzyme 2.4.1.145
adds_glycosyl_residueN-glycan_b-D-GlcpNAc_13