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libAnnotationSBML

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Neil Swainston
Neil Swainston
Tecnología
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libAnnotationSBML ,[object Object],[object Object],[object Object]
Introduction ,[object Object],[object Object],[object Object]
Purpose of annotations ,[object Object],[object Object],[object Object]
AnnotationWizard ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Annotating models: yeast ,[object Object],[object Object]
Project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE MeMo SABIO-RK Web service Web service Web service MeMo-RK
KineticsWizard
Project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE MeMo SABIO-RK Web service Web service Web service MeMo-RK
CellDesigner plugin
Purpose of annotations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Purpose of annotations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Isn’t ChEBI grrrreat … <species id=”glc&quot; name=&quot;D-Glucose&quot;> <annotation> <rdf:li rdf:resource=&quot;urn:miriam:obo.chebi:CHEBI:17634&quot;/> </annotation> </species>
libAnnotationSBML: what it does ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
MIRIAM UniProt ChEBI KEGG libAnnotationSBML SBase annotation OntologyTerm(s) Determine ontology Map to web service
OntologyTerm ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Purpose of annotations: to allow automation of tedious jobs D-Glyceraldehyde + NAD+ <=> D-Glycerate + NADH + H+
Purpose of annotations: to allow automation of tedious jobs ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Wish list ,[object Object],[object Object],[object Object]
Wish list ,[object Object],[object Object],[object Object],[object Object]
Finally … ,[object Object],[object Object],[object Object]
libAnnotationSBML ,[object Object],[object Object],[object Object]

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libAnnotationSBML

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  • 6. Project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE MeMo SABIO-RK Web service Web service Web service MeMo-RK
  • 8. Project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE MeMo SABIO-RK Web service Web service Web service MeMo-RK
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  • 12. Isn’t ChEBI grrrreat … <species id=”glc&quot; name=&quot;D-Glucose&quot;> <annotation> <rdf:li rdf:resource=&quot;urn:miriam:obo.chebi:CHEBI:17634&quot;/> </annotation> </species>
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  • 14. MIRIAM UniProt ChEBI KEGG libAnnotationSBML SBase annotation OntologyTerm(s) Determine ontology Map to web service
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  • 16. Purpose of annotations: to allow automation of tedious jobs D-Glyceraldehyde + NAD+ <=> D-Glycerate + NADH + H+
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