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.

1. Frank T. Bergmann (fbergman@u.washington.edu)

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. Systems Biology Workbench
http://sys-bio.org
3

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. Systems Biology Graphical
Notation (SBGN)
http://sbgn.org
5

6. Systems Biology Workbench
http://sys-bio.org
6

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
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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. 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. Outline
 EBI Web Services
 LibAnnotationSBML
 SAINT
10

11. EBI Web Services
http://www.ebi.ac.uk/Tools/webservices/
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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
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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. 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. 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
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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. LibAnnotationSBML
http://sbml.org/Community/Programs/libAnnotationSBML
17

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
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19. LibAnnotationSBML
http://www.slideshare.net/neilswainston/libannotationsbml
19

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. SAINT
http://saint-annotate.sourceforge.net/
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22. SAINT
http://shrinkster.com/1cqb
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23. SAINT
http://shrinkster.com/1cqb
23

24. SAINT
http://saint-annotate.sourceforge.net/
24

25. SAINT
http://shrinkster.com/1cqb
25

26. SAINT
http://shrinkster.com/1cqb
26

27. SAINT
http://shrinkster.com/1cqb
27

28. 28

29. SAINT
http://saint-annotate.sourceforge.net/
29

30. SAINT
http://saint-annotate.sourceforge.net/
30

31. SAINT
http://saint-annotate.sourceforge.net/
31

32. 32

33. CellDesigner
33

34. CellDesigner
34

35. CellDesigner
35

36. CellDesigner
36

37. COPASI
37

38. COPASI
38

39. 39

40. BioModels Import
40

41. Displaying Annotations
41

42. Displaying Annotations
42

43. Creating Annotations
43

44. 44

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
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