1. Access Reactome Database via Application Programming Interfaces (APIs) Guanming Wu Ontario Institute for Cancer Research

2. Reactome Data Model

4. Mapping into MySQL Database http://www.reactome.org/static_wordpress/objectrelational-mapping/

5. Mapping into MySQL Database http://www.reactome.org/static_wordpress/objectrelational-mapping/

6. Reactome APIs Java API Perl API SOAP API RESTful API

7. Reactome Curator Tool based on Java API

8. Get Reactome Data and Java API Download a mysql database dump file and load into a mysql database – sql Download the Reactome curator tool – reactome.jar: add it to your classpath – src.jar: Java source code for reactome.jar – mysql.jar: JDBC driver http://www.reactome.org/download/index.html

9. Java Data Model: Schema

10. Java Data Model: Class

11. Java Data Model: Attribute

12. Java Data Model: Instance

13. Java Data Model GKSchema GKSchemaClassGKSchemaAttribute GKInstance * classes * attributes * * owners +attributes 1 schemaClass

14. Connect to the Database

15. Use MySQLAdaptor Class

17. A Simple Fetch DatabaseObject +dbId:Long

18. Attribute based Query DatabaseObject +dbId:Long +displayName:String subclass Event Pathway subclass

19. Attribute based Query Operator may be “like” or others supported by SQL or mysql

20. Attribute based Query

21. DatabaseObject +dbId:Long +displayName:String Event Pathway subclass Species +name:String subclass 1..* +species subclass association

22. Attribute based Query

23. Complex Query

24. Reverse Attribute Query DatabaseObject +dbId:Long +displayName:String Event Pathway subclass Sepecies +name:String subclass 1..* +species 0..* hasEvent subclass association

25. Reverse Attribute Query

26. Another Reverse Attribute Query

27. Example: Get Reactions for a Protein ReactionlikeEventPhysicalEntity EntityWithAccessionedSequence CandidateSet ReferenceEntity +identifier:String 1 referenceEntity hasComponent 2..* hasMember hasCandidate 1..* input 0..* output Complex EntitySet GenomeEncodeEntity Ploymer repeatedUnit 1..* CatalystActivity catalystActivity 1 physicalEntity 1 Regulation regulatedEntity 1 regulator 1 subclass association

28. Example: Get Reactions for a Protein

30. ReferenceGeneProduct: [ReferenceGeneProduct:54208] UniProt:P00533 EGFR PhysicalEntity: 57 [EntityWithAccessionedSequence:1996343] p-6Y-EGFR M766_A767insASV mutant [plasma membrane] [EntityWithAccessionedSequence:1248649] Phospho-EGFRvIIImut [plasma membrane] [EntityWithAccessionedSequence:1996341] p-6Y-EGFR A289T mutant [plasma membrane] [EntityWithAccessionedSequence:1181399] EGFR E746_A750del;T790M mutant [plasma membrane] [EntityWithAccessionedSequence:1177532] EGFR G719A mutant [plasma membrane] [EntityWithAccessionedSequence:1996322] EGFR D770_N771insNPG mutant [plasma membrane] [EntityWithAccessionedSequence:1996326] EGFR M766_A767insASV mutant [plasma membrane] [EntityWithAccessionedSequence:1169418] EGFR G719S mutant [plasma membrane] [EntityWithAccessionedSequence:1228040] Phospho-EGFR L747_S752del mutant [plasma membrane] …… Reactions: 90 [Reaction:177944] Activation of SHP2 through the binding to phospho-Gab1 [Reaction:212713] Active PLC-gamma1 dissociates from EGFR [Reaction:183077] Assembly in clathrin-coated vesicles (CCVs) [Reaction:182994] Assembly of EGFR complex in clathrin-coated vesicles [Reaction:183002] Beta-Pix pushes CIN85 away from CBL [Reaction:183055] Binding of CBL to EGFR [Reaction:1225949] Binding of CBL to phosphorylated ligand-responsive EGFR mutants [Reaction:1220612] Binding of EGF to ligand-responsive EGFR mutants [Reaction:1306963] Binding of GRB2:GAB1 to p-ERBB2:p-EGFR ……

31. Get Instance Attribute Values

33. Pathway Diagram http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=69620&ID=141437&VID=6826841

34. Pathway Diagram: Data Model

36. Pathway Diagram: Color Protein

38. Pathway Diagram: Export to File

40. Disease Pathway: Data Model Disease identifier:String name:String Disease Ontology at EBI Event 0..* +disease PhysicalEntity 0..* +disease

41. Disease Pathway: Data Model PhysicalEntityEntityWithAccessionedSequenceGenomeEncodeEntity FragmentInsertionModification 0..* +hasModifiedResidue AbstractModifiedResidue GeneticallyModifiedResidue TranslationalModification FragmentModification CrosslinkedResidue FragmentDeletionModification GroupModifiedResidueModifiedResidue InterChainCrosslinkedResidue IntraChainCrosslinkedResidue ReplacedResidue subclass association

42. Disease Pathway: Data Model ReactionlikeEventEntityFunctionalStatus +disease ReactionlikeEvent normal +normalReaction 0..* +entityFunctionStatus 0..* PhysicalEntity +physicalEntity 1 1..* FunctionalStatus FunctionalStatusTypeSequenceOntology +functionalStatus +functionalStatusType1 +structuralVariant1

43. Disease Pathway: Visualization

48. Perl API

49. http://www.reactome.org/download/index.html

50. RESTful API http://www.reactome.org:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html

51. RESTful API http://www.reactome.org:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html

52. RESTful API http://www.reactome.org:8080/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html

53. SOAP API http://www.reactome.org:8080/caBIOWebApp/docs/services.html

54. SOAP API http://www.reactome.org:8080/caBIOWebApp/docs/caBIG_Reactome_User_Guide.pdf

55. Acknowledgements Java and Perl API Imre Vastrik David Croft RESTful API Stanislav Palatnik (GSoC) Disease model Marija Orlic-Milacic Karen Rothfels Robin Haw Lisa Matthew Bijay Jassai Heeyeon Song Marc Gillespie Steve Jupe Peter D’Eustachio Java and Perl API Imre Vastrik David Croft RESTful API Stanislav Palatnik (GSoC) Disease model Marija Orlic-Milacic Karen Rothfels Robin Haw Lisa Matthew Bijay Jassai Heeyeon Song Marc Gillespie Steve Jupe Peter D’Eustachio