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Access Reactome Database via Application Programming Interfaces (APIs)

Access Reactome Database via Application Programming Interfaces (APIs). Guanming Wu Ontario Institute for Cancer Research. Reactome Data Model. Reactome Data Model. Mapping into MySQL Database. http://www.reactome.org/static_wordpress/objectrelational-mapping/. Mapping into MySQL Database.

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Access Reactome Database via Application Programming Interfaces (APIs)

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

  2. Reactome Data Model

  3. 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 classes attributes * * * * GKSchemaClass GKSchemaAttribute owners attributes schemaClass 1 GKInstance +attributes

  14. Connect to the Database

  15. Use MySQLAdaptor Class

  16. Use MySQLAdaptor Class

  17. A Simple Fetch DatabaseObject +dbId:Long

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

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

  20. Attribute based Query

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

  22. Attribute based Query

  23. Complex Query

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

  25. Reverse Attribute Query

  26. Another Reverse Attribute Query

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

  28. Example: Get Reactions for a Protein

  29. Example: Get Reactions for a Protein

  30. Example: Get Reactions for a Protein 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

  32. 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

  35. Pathway Diagram: Data Model

  36. Pathway Diagram: Color Protein

  37. Pathway Diagram: Color Protein

  38. Pathway Diagram: Export to File

  39. Pathway Diagram: Export to File

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

  41. Disease Pathway: Data Model subclass GeneticallyModifiedResidue FragmentInsertionModification AbstractModifiedResidue FragmentModification CrosslinkedResidue TranslationalModification GroupModifiedResidue ModifiedResidue InterChainCrosslinkedResidue IntraChainCrosslinkedResidue FragmentDeletionModification ReplacedResidue association PhysicalEntity +hasModifiedResidue 0..* EntityWithAccessionedSequence GenomeEncodeEntity

  42. Disease Pathway: Data Model PhysicalEntity +physicalEntity 1 0..* 0..* ReactionlikeEvent ReactionlikeEvent EntityFunctionalStatus +normalReaction +entityFunctionStatus normal +disease 1..* +functionalStatus FunctionalStatus 1 +functionalStatusType +structuralVariant 1 FunctionalStatusType SequenceOntology

  43. Disease Pathway: Visualization

  44. Disease Pathway: Visualization

  45. Disease Pathway: Visualization

  46. Disease Pathway: Visualization

  47. Disease Pathway: Visualization

  48. Perl API

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

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

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