libAnnotationSBML <ul><li>Neil Swainston </li></ul><ul><li>Manchester Centre for Integrative Systems Biology </li></ul><ul...
Introduction <ul><li>Library ( not a tool ) for  linking annotated SBML  models to  MIRIAM  and related  web services </li...
Purpose of annotations <ul><li>Provide  definitive ,  unique identifier  for “stuff” </li></ul><ul><ul><li>One motivation:...
AnnotationWizard <ul><li>Shameless copy of Falko’s  semanticSBML </li></ul><ul><ul><li>See also  SAINT  (Allyson) </li></u...
Annotating models: yeast <ul><li>Genome-scale  SBML  model of yeast metabolism </li></ul><ul><ul><li>All 2153 molecules  h...
Project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model Parameters (K M , K cat ) Va...
KineticsWizard
Project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model Parameters (K M , K cat ) Va...
CellDesigner plugin
Purpose of annotations <ul><li>Provide definitive, unique identifier for “stuff” </li></ul><ul><ul><li>One motivation: map...
Purpose of annotations <ul><li>Easy question </li></ul><ul><ul><li>Is my model annotated? </li></ul></ul><ul><ul><li>Simpl...
Isn’t ChEBI grrrreat … <species id=”glc&quot; name=&quot;D-Glucose&quot;> <annotation> <rdf:li rdf:resource=&quot;urn:miri...
libAnnotationSBML: what it does <ul><li>Provides  unified interface  to following  web services : </li></ul><ul><ul><li>Ch...
MIRIAM UniProt ChEBI KEGG libAnnotationSBML SBase  annotation OntologyTerm(s) Determine ontology Map to web service
OntologyTerm <ul><li>Model components can be parsed to return  OntologyTerm s </li></ul><ul><li>OntologyTerms have the fol...
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 <ul><li>Suggest  corrections  to existing models </li></ul><ul...
Wish list <ul><li>Support more web services </li></ul><ul><li>Write it in C++ </li></ul><ul><li>WSDLs in MIRIAM?? </li></ul>
Wish list <ul><li>BUT  dynamic linking  of models to databases is still a little way off </li></ul><ul><ul><li>Web service...
Finally … <ul><li>Hopefully makes doing things with annotations easier </li></ul><ul><li>Have a look if you’re interested:...
libAnnotationSBML <ul><li>Neil Swainston </li></ul><ul><li>Manchester Centre for Integrative Systems Biology </li></ul><ul...
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libAnnotationSBML

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libAnnotationSBML

  1. 1. libAnnotationSBML <ul><li>Neil Swainston </li></ul><ul><li>Manchester Centre for Integrative Systems Biology </li></ul><ul><li>29 March 2009 </li></ul>
  2. 2. Introduction <ul><li>Library ( not a tool ) for linking annotated SBML models to MIRIAM and related web services </li></ul><ul><ul><li>Writing and reading of annotations </li></ul></ul><ul><li>Java – could be extended </li></ul>
  3. 3. Purpose of annotations <ul><li>Provide definitive , unique identifier for “stuff” </li></ul><ul><ul><li>One motivation: mapping experimental data to models </li></ul></ul><ul><ul><li>Need annotated models AND annotated data </li></ul></ul>
  4. 4. AnnotationWizard <ul><li>Shameless copy of Falko’s semanticSBML </li></ul><ul><ul><li>See also SAINT (Allyson) </li></ul></ul><ul><li>Principle: </li></ul><ul><ul><li>Iterate through model </li></ul></ul><ul><ul><li>Submit each species to an appropriate web service search facility ( ChEBI or UniProt ) </li></ul></ul><ul><ul><li>Prompt user for confirmation </li></ul></ul><ul><ul><li>Update model with annotation </li></ul></ul><ul><ul><li>Has also been wrapped as a web service itself </li></ul></ul>
  5. 5. Annotating models: yeast <ul><li>Genome-scale SBML model of yeast metabolism </li></ul><ul><ul><li>All 2153 molecules have MIRIAM annotations </li></ul></ul>
  6. 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
  7. 7. KineticsWizard
  8. 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
  9. 9. CellDesigner plugin
  10. 10. Purpose of annotations <ul><li>Provide definitive, unique identifier for “stuff” </li></ul><ul><ul><li>One motivation: mapping experimental data to models </li></ul></ul><ul><ul><li>Need annotated models AND annotated data </li></ul></ul><ul><ul><li>“ Tagging” </li></ul></ul><ul><li>More interesting purpose … </li></ul><ul><ul><li>Use the annotations to reason over the model </li></ul></ul>
  11. 11. Purpose of annotations <ul><li>Easy question </li></ul><ul><ul><li>Is my model annotated? </li></ul></ul><ul><ul><li>Simple answer: yes </li></ul></ul><ul><ul><li>Can be answered solely by libSBML </li></ul></ul><ul><li>More interesting question </li></ul><ul><ul><li>Is my model annotated well ? </li></ul></ul><ul><ul><li>Do my reactions elementally balance? </li></ul></ul><ul><ul><li>Simple answer may be yes or no, but harder to determine </li></ul></ul><ul><ul><li>Can’t be determined solely by libSBML </li></ul></ul>
  12. 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>
  13. 13. libAnnotationSBML: what it does <ul><li>Provides unified interface to following web services : </li></ul><ul><ul><li>ChEBI </li></ul></ul><ul><ul><li>KEGG </li></ul></ul><ul><ul><li>UniProt </li></ul></ul><ul><ul><li>SBO </li></ul></ul><ul><ul><li>others… </li></ul></ul><ul><li>Wraps these calls so that it appears that you are accessing these locally </li></ul>
  14. 14. MIRIAM UniProt ChEBI KEGG libAnnotationSBML SBase annotation OntologyTerm(s) Determine ontology Map to web service
  15. 15. OntologyTerm <ul><li>Model components can be parsed to return OntologyTerm s </li></ul><ul><li>OntologyTerms have the following interface: </li></ul><ul><li>Development of tools to exploit annotations becomes greatly simplified: </li></ul><ul><ul><li>OntologyTerm[] ots = sbmlUtils.getOntologyTerms( sbase ); </li></ul></ul><ul><ul><li>OntologyTerm ot = ots[0]; </li></ul></ul><ul><ul><li>ot.getName(); ot.getSynonyms(); ot.getFormula(); </li></ul></ul>
  16. 16. Purpose of annotations: to allow automation of tedious jobs D-Glyceraldehyde + NAD+ <=> D-Glycerate + NADH + H+
  17. 17. Purpose of annotations: to allow automation of tedious jobs <ul><li>Suggest corrections to existing models </li></ul><ul><ul><li>Incorrect annotations </li></ul></ul><ul><ul><li>Missing reactants / products </li></ul></ul><ul><ul><li>Stoichiometry </li></ul></ul><ul><li>Better still: intelligent generation of models ? </li></ul><ul><ul><li>AutoComplete? </li></ul></ul>
  18. 18. Wish list <ul><li>Support more web services </li></ul><ul><li>Write it in C++ </li></ul><ul><li>WSDLs in MIRIAM?? </li></ul>
  19. 19. Wish list <ul><li>BUT dynamic linking of models to databases is still a little way off </li></ul><ul><ul><li>Web services are inconsistent </li></ul></ul><ul><ul><ul><li>getName()? getDescription()? getTitle()? </li></ul></ul></ul><ul><ul><ul><li>Semantic web services needed </li></ul></ul></ul>
  20. 20. Finally … <ul><li>Hopefully makes doing things with annotations easier </li></ul><ul><li>Have a look if you’re interested: </li></ul><ul><ul><li>http://mcisb.sourceforge.net </li></ul></ul>
  21. 21. libAnnotationSBML <ul><li>Neil Swainston </li></ul><ul><li>Manchester Centre for Integrative Systems Biology </li></ul><ul><li>29 March 2009 </li></ul>

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