Computational Tools For The Annotation of SBML Models

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I was asked to give a brief talk in a Seminar (Semantic Web in Biomedicine), on computational tools that make the task of using all the great ontologies (like MIRIAM, SBO, ChEBI, UniProt, KEGG) that we have come to love easier.

In the presentation I introduce several of the Web Services at the EBI, libAnnotationSBML and SAINT.

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Computational Tools For The Annotation of SBML Models

  1. 1. Frank T. Bergmann (fbergman@u.washington.edu)
  2. 2. Systems Biology Workbench Module 3 SBW C# Binding SBW Java Binding Module 2 SBW Broker Module 1 SBW C++ Binding SBW C++ Binding Module 1 SBW Java Binding Module 2 SBW Broker SBW C# Binding Module 3 http://sys-bio.org 2
  3. 3. Systems Biology Workbench http://sys-bio.org 3
  4. 4. Systems Biology Markup Language (SBML) <?xml version="1.0" encoding="UTF-8"?> <sbml xmlns = "http://www.sbml.org/sbml/level2" level = "2" <model id = "oscli" name = "Oscli (Heinrich model)"> <listOfCompartments> <compartment id = "compartment" size = "1"/> </listOfCompartments> <listOfSpecies> <species id = "S1“ initialConcentration = "0" comp <species id = "S2“ initialConcentration = "1" comp <species id = "X0" boundaryCondition = "true" init <species id = "X1" boundaryCondition = "true" init <species id = "X2" boundaryCondition = "true" init </listOfSpecies> <listOfParameters> <parameter id = "J0_v0" value = "8"/> <parameter id = "J1_k3" value = "0"/> <parameter id = "J2_k1" value = "1"/> <parameter id = "J2_k_1" value = "0"/> <parameter id = "J2_c" value = "1"/> <parameter id = "J2_q" value = "3"/> <parameter id = "J3_k2" value = "5"/> </listOfParameters> <listOfReactions> <reaction id = "J0" reversible = "false"> <listOfReactants> <speciesReference species = "X0" stoichiometry </listOfReactants> <listOfProducts> <speciesReference species = "S1" stoichiometry </listOfProducts> <kineticLaw> <math xmlns = "http://www.w3.org/1998/Math/M <ci> J0_v0 </ci> </math> </kineticLaw> </reaction> [ . . . ] 4
  5. 5. Systems Biology Graphical Notation (SBGN) http://sbgn.org 5
  6. 6. Systems Biology Workbench http://sys-bio.org 6
  7. 7. Systems Biology Ontology Quantitative Roles of Precise List of parameters reaction classification simulation Entity Interaction used in participants of rate laws frameworks biochemistry Macromolecule Reaction Substrate Hill coefficient Hill function Discrete Non-covalent Control complex Biochemical Simple chemical process First order Michaelis Catalyst reversible math Continuous constant action kinetics Empty set Combination 7
  8. 8. MIRIAM [...] <species metaid="metaid_0000006" id="L_EGFR" compartment="compartment" initialConcentration="0"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22rdfsyntaxns#" xmlns:bqbiol="http://biomodels.net/biologyqualifiers/"> <rdf:Description rdf:about="#metaid_0000006"> <bqbiol:hasPart> <rdf:Bag> <rdf:li rdf:resource="http://www.uniprot.org/#P07522" /> <rdf:li rdf:resource="http://www.uniprot.org/#Q9QX70_RAT" /> </rdf:Bag> </bqbiol:hasPart> </rdf:Description> </rdf:RDF> </annotation> </species> [...]
  9. 9. MIRIAM [...] <species metaid="metaid_0000006" id="L_EGFR" compartment="compartment" initialConcentration="0"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22rdfsyntaxns#" xmlns:bqbiol="http://biomodels.net/biologyqualifiers/"> <rdf:Description rdf:about="#metaid_0000006"> <bqbiol:hasPart> <rdf:Bag> <rdf:li rdf:resource="http://www.uniprot.org/#P07522" /> <rdf:li rdf:resource="http://www.uniprot.org/#Q9QX70_RAT" /> </rdf:Bag> </bqbiol:hasPart> </rdf:Description> </rdf:RDF> </annotation> </species> [...]
  10. 10. Outline  EBI Web Services  LibAnnotationSBML  SAINT 10
  11. 11. EBI Web Services http://www.ebi.ac.uk/Tools/webservices/ 11
  12. 12. BioModels WebService  getAllCuratedModelsId  getModelsIdByTaxonomyId  getAllModelsId  getModelsIdByUniprot  getAllNonCuratedModelsId  getModelsIdByUniprotId  getEndPoint  getModelsIdByUniprotIds  getModelNameById  getSimpleModelById  getModelSBMLById  getSimpleModelsByChEBIIds  getModelsIdByChEBI  getSimpleModelsByReactomeIds  getModelsIdByChEBIId  getSimpleModelsByUniprotIds  getModelsIdByGO  getSimpleModelsRelatedWithChEB I  getModelsIdByGOId  getModelsIdByName  getModelsIdByPerson  getModelsIdByPublication  getModelsIdByTaxonomy 12
  13. 13. MIRIAM WebService  checkRegExp  getNames  getDataResources  getOfficialDataTypeURI  getDataTypeDef  getResourceInfo  getDataTypePattern  getResourceInstitution  getDataTypeSynonyms  getResourceLocation  getDataTypeURI  getServicesInfo  getDataTypeURIs  getServicesVersion  getDataTypesId  getURI  getDataTypesName  isDeprecated  getLocation  isLibraryUpdated  getLocations  getLocations  getMiriamURI  getName 13
  14. 14. OntologyLookup WebService  getVersion();  getTermById(String termId, String ontologyName);  getTermMetadata(String termId, String ontologyName);  getTermXrefs(String termId, String ontologyName);  getOntologyNames();  getOntologyLoadDate(String ontologyName);  getAllTermsFromOntology(String ontologyName);  getRootTerms(String ontologyName);  getTermsByName(String partialName, String ontologyName, boolean reverseKeyOrder);  getPrefixedTermsByName(String partialName, boolean reverseKeyOrder);  getTermParents(String termId, String ontologyName);  getTermChildren(String termId, String ontologyName, int distance, int[] relationTypes);  getTermRelations(String termId, String ontologyName);  getChildrenFromRoot(String termId, String ontologyName, Vector childrenIds);  isObsolete(String termId, String ontologyName);  getTermsByAnnotationData(String ontologyName, String annotationType, String strValue, Double fromDblValue, Double toDblValue); 14
  15. 15. SBO WebService  getTermById  getStringTermById  searchPossibleCompletions  searchStringPossibleCompletions  getTree  getStringTree  searchTermSynonyms  searchStringTermSynonyms  searchTermDetails  searchStringTermDetails  searchTermMath  searchStringTermMath  searchTermName  searchStringTermName  getTermsByIds  getStringTermsByIds  getTermByIdOWL  searchString  searchPossibleCompletionsOWL  isDirectChildOf  getTreeOWL  isChildOf  searchTermSynonymsOWL  isObsolete  searchTermDetailsOWL  search  searchTermMathOWL  isRoot  searchTermNameOWL  getTermsByIdsOWL  searchOWL 15
  16. 16. EBI Web Service  Java Clients exist for all services  Documentation is sparse, however method calls are intuitive  WSDL files work fine with .NET  16
  17. 17. LibAnnotationSBML http://sbml.org/Community/Programs/libAnnotationSBML 17
  18. 18. LibAnnotationSBML  Java – Library for Reading / Writing Annotations for SBML files using  ChEBI  SBO  MIRIAM  KEGG  UniProt  All wrapped into one unified API http://sbml.org/Community/Programs/libAnnotationSBML 18
  19. 19. LibAnnotationSBML http://www.slideshare.net/neilswainston/libannotationsbml 19
  20. 20. LibAnnotationSBML  Several Examples using LibAnnotationSBML exist today:  SbmlReactionBalancer: determines whether the reactions specified within an SBML file are elementally balanced (retrieves formulae of reaction participants)  AnnotationWizard / AutoCompleter provides OntologyTerms for a given name http://sbml.org/Community/Programs/libAnnotationSBML 20
  21. 21. SAINT http://saint-annotate.sourceforge.net/ 21
  22. 22. SAINT http://shrinkster.com/1cqb 22
  23. 23. SAINT http://shrinkster.com/1cqb 23
  24. 24. SAINT http://saint-annotate.sourceforge.net/ 24
  25. 25. SAINT http://shrinkster.com/1cqb 25
  26. 26. SAINT http://shrinkster.com/1cqb 26
  27. 27. SAINT http://shrinkster.com/1cqb 27
  28. 28. 28
  29. 29. SAINT http://saint-annotate.sourceforge.net/ 29
  30. 30. SAINT http://saint-annotate.sourceforge.net/ 30
  31. 31. SAINT http://saint-annotate.sourceforge.net/ 31
  32. 32. 32
  33. 33. CellDesigner 33
  34. 34. CellDesigner 34
  35. 35. CellDesigner 35
  36. 36. CellDesigner 36
  37. 37. COPASI 37
  38. 38. COPASI 38
  39. 39. 39
  40. 40. BioModels Import 40
  41. 41. Displaying Annotations 41
  42. 42. Displaying Annotations 42
  43. 43. Creating Annotations 43
  44. 44. 44
  45. 45. Credit where Credit is due  the libAnnotationSBML UML slide comes from Neil’s slideshare:  http://www.slideshare.net/neilswainston/liban notationsbml  Most of the SAINT slides come from Allyson’s slideshare:  http://shrinkster.com/1cqb 45

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